diff --git a/.Rbuildignore b/.Rbuildignore index c3c4aec..497df46 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -6,3 +6,5 @@ ^codecov\.yml$ ^data-raw$ ^R/abx_index_old\.R$ +^\.github$ +^.*\.Rproj$ diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..0f2fe08 --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,52 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + branches: [main, master] + +name: R-CMD-check + +permissions: read-all + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: macos-latest, r: 'release'} + - {os: windows-latest, r: 'release'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml new file mode 100644 index 0000000..fefc52e --- /dev/null +++ b/.github/workflows/test-coverage.yaml @@ -0,0 +1,61 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main, master] + pull_request: + branches: [main, master] + +name: test-coverage + +permissions: read-all + +jobs: + test-coverage: + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::covr, any::xml2 + needs: coverage + + - name: Test coverage + run: | + cov <- covr::package_coverage( + quiet = FALSE, + clean = FALSE, + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") + ) + covr::to_cobertura(cov) + shell: Rscript {0} + + - uses: codecov/codecov-action@v4 + with: + fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} + file: ./cobertura.xml + plugin: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + + - name: Show testthat output + if: always() + run: | + ## -------------------------------------------------------------------- + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash + + - name: Upload test results + if: failure() + uses: actions/upload-artifact@v4 + with: + name: coverage-test-failures + path: ${{ runner.temp }}/package diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 4d3c092..0000000 --- a/.travis.yml +++ /dev/null @@ -1,14 +0,0 @@ -# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r - -language: R -cache: packages -warnings_are_errors: true - -os: - - linux - - osx - -r: - - 3.6 - - release - - devel diff --git a/DESCRIPTION b/DESCRIPTION index 3afb9be..c5b0372 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,16 +3,19 @@ Title: Modeling the Susceptibility of a Bacterial Community to Antibiotics Version: 0.0.1.0 Author: Vincent Tu Maintainer: Vincent Tu -Description: This package calculates an index for a given bacterial community's susceptibility to the specified antibiotics. +Description: Calculates an index for a given bacterial community's susceptibility to specified antibiotics. License: GPL-3 Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.2 +RoxygenNote: 7.2.3 Suggests: knitr, rmarkdown, covr, testthat -Depends: +Depends: R (>= 2.10) +Imports: + whatbacteria +Remotes: PennChopMicrobiomeProgram/whatbacteria diff --git a/NAMESPACE b/NAMESPACE index 57ccd17..748e543 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -14,3 +14,4 @@ export(mirix_metronidazole) export(mirix_vancomycin) export(phenotype_susceptibility) export(predict_abundance) +import(whatbacteria) diff --git a/R/abx_index.R b/R/abx_index.R index 4d799ad..a2b0f8b 100644 --- a/R/abx_index.R +++ b/R/abx_index.R @@ -24,8 +24,8 @@ NULL mirix_vancomycin <- function(abundance, lineage, replace_zero = 1e-4, - antibiotic_db = taxon_susceptibility, - phenotype_db = taxon_phenotypes) { + antibiotic_db = whatbacteria::taxon_susceptibility, + phenotype_db = whatbacteria::taxon_phenotypes) { susceptibility <- antibiotic_susceptibility_vancomycin( lineage, antibiotic_db, phenotype_db) mirix(abundance, susceptibility, replace_zero) @@ -36,7 +36,7 @@ mirix_vancomycin <- function(abundance, mirix_doxycycline <- function(abundance, lineage, replace_zero = 1e-4, - antibiotic_db = taxon_susceptibility) { + antibiotic_db = whatbacteria::taxon_susceptibility) { susceptibility <- antibiotic_susceptibility_tetracycline( lineage, antibiotic_db) mirix(abundance, susceptibility, replace_zero) @@ -47,7 +47,7 @@ mirix_doxycycline <- function(abundance, mirix_amoxicillin <- function(abundance, lineage, replace_zero = 1e-4, - antibiotic_db = taxon_susceptibility) { + antibiotic_db = whatbacteria::taxon_susceptibility) { susceptibility <- antibiotic_susceptibility_penicillin( lineage, antibiotic_db) mirix(abundance, susceptibility, replace_zero) @@ -58,7 +58,7 @@ mirix_amoxicillin <- function(abundance, mirix_metronidazole <- function(abundance, lineage, replace_zero = 1e-4, - phenotype_db = taxon_phenotypes) { + phenotype_db = whatbacteria::taxon_phenotypes) { susceptibility <- phenotype_susceptibility( lineage = lineage, phenotype = "aerobic_status", @@ -75,7 +75,7 @@ mirix_metronidazole <- function(abundance, mirix_ciprofloxacin <- function(abundance, lineage, replace_zero = 1e-4, - phenotype_db = taxon_phenotypes) { + phenotype_db = whatbacteria::taxon_phenotypes) { susceptibility <- phenotype_susceptibility( lineage = lineage, phenotype = "aerobic_status", @@ -92,8 +92,8 @@ mirix_ciprofloxacin <- function(abundance, mirix_gentamicin <- function(abundance, lineage, replace_zero = 1e-4, - antibiotic_db = taxon_susceptibility, - phenotype_db = taxon_phenotypes) { + antibiotic_db = whatbacteria::taxon_susceptibility, + phenotype_db = whatbacteria::taxon_phenotypes) { susceptibility <- antibiotic_susceptibility_aminoglycoside( lineage, antibiotic_db, phenotype_db) mirix(abundance, susceptibility, replace_zero) @@ -111,6 +111,7 @@ mirix_gentamicin <- function(abundance, #' 0.5 is typical. For relative abundances, a number that is slightly lower #' than the lowest relative abundance will work. #' +#' @import whatbacteria #' @return The MiRIx value #' @export mirix <- function (abundance, susceptibility, replace_zero = 1e-4) { diff --git a/R/data.R b/R/data.R index e4136ff..261a7f0 100644 --- a/R/data.R +++ b/R/data.R @@ -1,31 +1,3 @@ -#' Gram stain and aerobic status of bacterial taxa -#' @format A data frame with the following columns: -#' \describe{ -#' \item{taxon}{The name of the taxon} -#' \item{rank}{The rank of the taxon} -#' \item{aerobic_status}{ -#' The aerobic status. One of "aerobe", "facultative anaerobe", or -#' "obligate anaerobe".} -#' \item{gram_stain}{ -#' How the taxon appears when Gram-stained. One of "Gram-positive" or -#' "Gram-negative".} -#' \item{doi}{DOI of the publication from which the information was obtained.} -#' } -"taxon_phenotypes" - -#' Antibiotic susceptibility of bacterial taxa -#' @format A data frame with the following columns: -#' \describe{ -#' \item{taxon}{The name of the taxon} -#' \item{rank}{The rank of the taxon} -#' \item{antibiotic}{The antibiotic or antibiotic class} -#' \item{value}{ -#' The susceptibility of the taxon to the antibiotic, one of "susceptible" -#' or "resistant".} -#' \item{doi}{DOI of the publication from which the information was obtained.} -#' } -"taxon_susceptibility" - #' Example data from Weiss et al. #' #' @format A data frame with the following columns: diff --git a/R/match.R b/R/match.R index f296951..29bb56a 100644 --- a/R/match.R +++ b/R/match.R @@ -28,12 +28,8 @@ #' @export antibiotic_susceptibility <- function (lineage, antibiotic, - db = taxon_susceptibility) { - is_relevant <- db$antibiotic %in% antibiotic - db <- db[is_relevant, c("taxon", "rank", "value")] - - susceptibility_values <- match_annotation(lineage, db) - susceptibility_values + db = whatbacteria::taxon_susceptibility) { + whatbacteria::what_antibiotic(lineage, antibiotic, db) } #' Evaluate antibiotic susceptibility based on phenotype @@ -74,107 +70,9 @@ antibiotic_susceptibility <- function (lineage, phenotype_susceptibility <- function (lineage, phenotype, susceptibility, - db = taxon_phenotypes) { - is_relevant <- db[[phenotype]] %in% names(susceptibility) - db <- db[is_relevant, c("taxon", "rank", phenotype)] - # match_annotation() requires a column named "value" - colnames(db)[3] <- "value" - - phenotype_values <- match_annotation(lineage, db) - + db = whatbacteria::taxon_phenotypes) { + phenotype_values <- whatbacteria::what_phenotype(lineage, phenotype, db) susceptibility_values <- susceptibility[phenotype_values] susceptibility_values <- unname(susceptibility_values) susceptibility_values } - -# Determine the annotation values for each lineage -# -# @param lineage A vector of taxonomic assignments or lineages -# @param db A data frame with columns named "taxon", "rank", and "value" -# @return A vector of assigned values -match_annotation <- function (lineage, db) { - get_rank_specific_db <- function (r) { - rank_is_r <- db[["rank"]] %in% r - db[rank_is_r,] - } - db_ranks <- lapply(rev(taxonomic_ranks), get_rank_specific_db) - names(db_ranks) <- rev(taxonomic_ranks) - - get_values_by_rank <- function (rank_specific_db) { - taxa_idx <- match_taxa(lineage, rank_specific_db[["taxon"]]) - rank_specific_db[["value"]][taxa_idx] - } - values_by_rank <- vapply( - db_ranks, - get_values_by_rank, - rep("a", length(lineage))) - - if (length(lineage) == 1) { - assigned_values <- first_non_na_value(values_by_rank) - } else { - assigned_values <- apply(values_by_rank, 1, first_non_na_value) - } - assigned_values -} - -# The 'official' taxonomic ranks supported by this package -taxonomic_ranks <- c( - "Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species") - -# Return the first value that is not NA. If all values are NA, return NA. The -# resultant vector will not have names. -first_non_na_value <- function (x) { - unname(x[first_true_idx(!is.na(x))]) -} - -# For each lineage, return the index of the taxon that is found within the -# lineage. If no taxa are found, return NA for that element. If multiple taxa -# are found, we issue a warning and return the index of the first taxon in the -# vector of taxa. -match_taxa <- function (lineages, taxa) { - n_lineages <- length(lineages) - if (length(taxa) == 0) { - return(rep_len(NA_character_, length(lineages))) - } - - taxa_patterns <- paste0("(?<=__|\\b)(?:", taxa, ")\\b") - lineage_matches <- vapply( - X = taxa_patterns, - FUN = grepl, - FUN.VALUE = rep_len(TRUE, n_lineages), - x = lineages, - perl = TRUE, - USE.NAMES = TRUE) - - # If the user passes only one lineage, lineage_matches will be a vector - # rather than an array. After some trial and error, I found that it's better - # to deal with this at each stage of the computation, rather than trying to - # coerce the vector to an array up front. - if (n_lineages == 1) { - multi_matches <- sum(lineage_matches) > 1 - } else { - multi_matches <- rowSums(lineage_matches) > 1 - } - if (any(multi_matches)) { - warning( - "The following lineages match more than one taxon:\n", - paste(lineages[multi_matches], collapse = "\n"), "\n") - } - - if (n_lineages == 1) { - taxon_idx <- first_true_idx(lineage_matches) - } else { - taxon_idx <- apply(lineage_matches, 1, first_true_idx) - } - taxon_idx -} - -# Return the first index of a boolean vector that is TRUE. If all elements of -# the vector are FALSE, return NA. Tempted to call this function minwhich. -first_true_idx <- function (x) { - if (any(x)) { - min(which(x == TRUE)) - } else { - NA_integer_ - } -} diff --git a/R/predict.R b/R/predict.R index 2e21051..1c61066 100644 --- a/R/predict.R +++ b/R/predict.R @@ -1,7 +1,7 @@ #' Predict taxon abundances at given values of an index #' #' @param index_value Value or values of the index at which to make predictions. -#' @param abundances A vector of taxon abundances in a sample. +#' @param abundance A vector of taxon abundances in a sample. #' @param susceptibility A character vector of antibiotic susceptibility, with #' values that are "susceptible", "resistant", or \code{NA}. #' @return A new vector of abundances if \code{index_value} has length 1. If diff --git a/R/susceptibility.R b/R/susceptibility.R index 850cf77..3ee45df 100644 --- a/R/susceptibility.R +++ b/R/susceptibility.R @@ -13,8 +13,8 @@ NULL #' @rdname antibiotic_specific_susceptibility #' @export antibiotic_susceptibility_vancomycin <- function (lineage, - antibiotic_db = taxon_susceptibility, - phenotype_db = taxon_phenotypes) { + antibiotic_db = whatbacteria::taxon_susceptibility, + phenotype_db = whatbacteria::taxon_phenotypes) { # Gram-positive organisms are susceptible to vancomycin ph_sus <- phenotype_susceptibility( lineage = lineage, @@ -33,7 +33,7 @@ antibiotic_susceptibility_vancomycin <- function (lineage, #' @rdname antibiotic_specific_susceptibility #' @export antibiotic_susceptibility_tetracycline <- function (lineage, - antibiotic_db = taxon_susceptibility) { + antibiotic_db = whatbacteria::taxon_susceptibility) { intrinsic_sus <- rep("susceptible", length(lineage)) abx_sus <- antibiotic_susceptibility( lineage = lineage, @@ -45,7 +45,7 @@ antibiotic_susceptibility_tetracycline <- function (lineage, #' @rdname antibiotic_specific_susceptibility #' @export antibiotic_susceptibility_penicillin <- function(lineage, - antibiotic_db = taxon_susceptibility) { + antibiotic_db = whatbacteria::taxon_susceptibility) { intrinsic_sus <- rep("susceptible", length(lineage)) abx_sus <- antibiotic_susceptibility( lineage = lineage, @@ -57,15 +57,15 @@ antibiotic_susceptibility_penicillin <- function(lineage, #' @rdname antibiotic_specific_susceptibility #' @export antibiotic_susceptibility_aminoglycoside <- function (lineage, - antibiotic_db = taxon_susceptibility, - phenotype_db = taxon_phenotypes) { - gram_stain_db <- taxon_phenotypes[,c("taxon", "rank", "gram_stain")] + antibiotic_db = whatbacteria::taxon_susceptibility, + phenotype_db = whatbacteria::taxon_phenotypes) { + gram_stain_db <- whatbacteria::taxon_phenotypes[,c("taxon", "rank", "gram_stain")] colnames(gram_stain_db)[3] <- "value" - gram_stain_phenotype <- match_annotation(lineage, gram_stain_db) + gram_stain_phenotype <- whatbacteria::match_annotation(lineage, gram_stain_db) - aerobic_status_db <- taxon_phenotypes[,c("taxon", "rank", "aerobic_status")] + aerobic_status_db <- whatbacteria::taxon_phenotypes[,c("taxon", "rank", "aerobic_status")] colnames(aerobic_status_db)[3] <- "value" - aerobic_status_phenotype <- match_annotation(lineage, aerobic_status_db) + aerobic_status_phenotype <- whatbacteria::match_annotation(lineage, aerobic_status_db) combined_phenotype <- ifelse( is.na(gram_stain_phenotype) | is.na(aerobic_status_phenotype), diff --git a/README.Rmd b/README.Rmd index b7b80f4..318f5c2 100644 --- a/README.Rmd +++ b/README.Rmd @@ -17,6 +17,11 @@ devtools::load_all() # mirix + +[![R-CMD-check](https://github.com/PennChopMicrobiomeProgram/mirix/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/PennChopMicrobiomeProgram/mirix/actions/workflows/R-CMD-check.yaml) +[![codecov](https://codecov.io/gh/PennChopMicrobiomeProgram/mirix/graph/badge.svg?token=7DBBaNoGDc)](https://codecov.io/gh/PennChopMicrobiomeProgram/mirix) + + The goal of mirix is to calculate the Microbiome Response Index (MiRIx) for a given bacterial community. Often this will be used to predict the community's susceptibility to an antibiotic. @@ -154,7 +159,7 @@ human microbiome. It is here where we note that the *Firmicutes* are generally Gram-positive. ```{r} -taxon_phenotypes %>% +whatbacteria::taxon_phenotypes %>% filter(taxon %in% "Firmicutes") ``` @@ -164,7 +169,7 @@ where we note that *Lactobacillus* species are typically resistant to vancomycin. ```{r} -taxon_susceptibility %>% +whatbacteria::taxon_susceptibility %>% filter(taxon %in% "Lactobacillus") ``` diff --git a/README.md b/README.md index ce60db8..0c62245 100644 --- a/README.md +++ b/README.md @@ -1,290 +1,296 @@ - - - -# mirix - -The goal of mirix is to calculate the Microbiome Response Index (MiRIx) -for a given bacterial community. Often this will be used to predict the -community’s susceptibility to an antibiotic. - -## Installation - -You can install the development version of mirix with `devtools`: - -``` r -#install.packages("devtools") -devtools::install_github("PennChopMicrobiomeProgram/mirix") -``` - -## Calculating antibiotic index values - -Here, we’ll load the `mirix` package, demonstrate some basic tasks, and -give some pointers for its use. Although we could accomplish all our -tasks in base R, the `mirix` package works very nicely with functions -from the tidyverse. We’ll import those functions now. - -``` r -library(tidyverse) -``` - -Next, we’ll load the `mirix` library. - -``` r -library(mirix) -``` - -This package comes with a built-in data set, `weiss2021_data`, from a -study of the gut microbiota in children with sepsis (PMID 33786436). The -children in this study were exposed to a range of antibiotics, and fecal -samples were collected across a series of time windows after diagnosis -(`study_window` A-E). Bacterial communities in the fecal samples were -profiled by sequencing the 16S rRNA gene, which serves as a fingerprint -to identify bacteria in each sample. The study included samples from a -set of healthy children in a similar age group for comparison. Here is a -summary of the number of samples in each time window: - -``` r -weiss2021_data %>% - distinct(sample_id, study_group, study_window) %>% - count(study_group, study_window) %>% - knitr::kable() -``` - -| study_group | study_window | n | -|:------------|:-------------|----:| -| Healthy | NA | 44 | -| Sepsis | A | 17 | -| Sepsis | B | 9 | -| Sepsis | C | 7 | -| Sepsis | D | 2 | -| Sepsis | E | 8 | - -for each sample collected, the data frame contains the relative -abundance of all bacteria with a proportion of more than 0.001. Here is -one of the sepsis samples, from subject 19019 in time window A. In this -sample, the sequencing results indicated the following types of -bacteria: - -``` r -weiss2021_data %>% - filter(sample_id %in% "Sepsis.19019.A") %>% - select(lineage, proportion) %>% - knitr::kable() -``` - -| lineage | proportion | -|:---------------------------------------------------------------------------------------------------------------------------------|-----------:| -| k\_\_Bacteria; p\_\_Firmicutes; c\_\_Bacilli; o\_\_Lactobacillales; f\_\_Enterococcaceae; g\_\_Enterococcus | 0.5491550 | -| k\_\_Bacteria; p\_\_Firmicutes; c\_\_Bacilli; o\_\_Lactobacillales; f\_\_Lactobacillaceae | 0.3418542 | -| k\_\_Bacteria; p\_\_Proteobacteria; c\_\_Gammaproteobacteria; o\_\_Pseudomonadales; f\_\_Pseudomonadaceae; g\_\_Pseudomonas | 0.0825587 | -| k\_\_Bacteria; p\_\_Proteobacteria; c\_\_Gammaproteobacteria; o\_\_Enterobacteriales; f\_\_Enterobacteriaceae | 0.0094255 | -| k\_\_Bacteria; p\_\_Proteobacteria; c\_\_Gammaproteobacteria; o\_\_Xanthomonadales; f\_\_Xanthomonadaceae; g\_\_Stenotrophomonas | 0.0069635 | -| k\_\_Bacteria; p\_\_Firmicutes; c\_\_Bacilli; o\_\_Bacillales; f\_\_Staphylococcaceae; g\_\_Staphylococcus | 0.0051231 | -| k\_\_Bacteria; p\_\_Actinobacteria; c\_\_Actinobacteria; o\_\_Actinomycetales; f\_\_Propionibacteriaceae | 0.0027708 | - -For each type of bacteria, the taxonomic assignment includes all the -taxon names from the kingdom on down to the most specific taxon that -could be determined from the sequence, in most cases the genus. -Following the [NCBI taxonomy -browser](https://www.ncbi.nlm.nih.gov/taxonomy), we call this result the -lineage. - -Our goal will be to use the lineage information to predict which -bacteria in each sample would be susceptible or resistant to various -antibiotics. For a given antibiotic, we construct an -*antibiotic-specific* Mircrobiome Response Index by taking the log-ratio -of the abundance for resistant organisms over that of susceptible -organisms. - -If the bacterial community is dominated by susceptible organisms, the -index will be negative. Conversely, the index is positive if susceptible -organisms constitute a minority. If an antibiotic has the predicted -effect on a bacterial community, the index should increase after the -antibiotic is introduced. - -Let’s compute the vancomycin response index for each sample in the -study. - -``` r -weiss2021_vanc <- weiss2021_data %>% - group_by(sample_id, study_group, study_window) %>% - summarise(vanc = mirix_vancomycin(proportion, lineage), .groups = "drop") - -weiss2021_vanc %>% - ggplot(aes(x=study_window, y = vanc)) + - geom_boxplot() + - facet_grid(~ study_group, scales = "free_x", space = "free_x") + - labs(x = "Study window", y = "Vancomycin-specific index") -``` - -![](tools/readme/weiss_vancomycin_index-1.png) - -For healthy children, the medain value of the index is about 0.2, -whereas it is roughly 0.85 across the samples from children with sepsis. -Let’s look further into how the index was calculated, and check out -which bacteria were labeled as susceptible or resistant to vancomycin. - -## Susceptible and resistant bacteria - -The `mirix` library offers some lower-level functions that show more -details about how the index was calculated. For each antibiotic with an -index function, there is an accompanying function to determine the -susceptibility for each lineage. Let’s list out the susceptibility for -the lineages in the sample from subject 19019: - -``` r -weiss2021_data %>% - filter(sample_id %in% "Sepsis.19019.A") %>% - mutate(susceptibility = antibiotic_susceptibility_vancomycin(lineage)) %>% - select(lineage, susceptibility) %>% - knitr::kable() -``` - -| lineage | susceptibility | -|:---------------------------------------------------------------------------------------------------------------------------------|:---------------| -| k\_\_Bacteria; p\_\_Firmicutes; c\_\_Bacilli; o\_\_Lactobacillales; f\_\_Enterococcaceae; g\_\_Enterococcus | susceptible | -| k\_\_Bacteria; p\_\_Firmicutes; c\_\_Bacilli; o\_\_Lactobacillales; f\_\_Lactobacillaceae | susceptible | -| k\_\_Bacteria; p\_\_Proteobacteria; c\_\_Gammaproteobacteria; o\_\_Pseudomonadales; f\_\_Pseudomonadaceae; g\_\_Pseudomonas | resistant | -| k\_\_Bacteria; p\_\_Proteobacteria; c\_\_Gammaproteobacteria; o\_\_Enterobacteriales; f\_\_Enterobacteriaceae | resistant | -| k\_\_Bacteria; p\_\_Proteobacteria; c\_\_Gammaproteobacteria; o\_\_Xanthomonadales; f\_\_Xanthomonadaceae; g\_\_Stenotrophomonas | resistant | -| k\_\_Bacteria; p\_\_Firmicutes; c\_\_Bacilli; o\_\_Bacillales; f\_\_Staphylococcaceae; g\_\_Staphylococcus | susceptible | -| k\_\_Bacteria; p\_\_Actinobacteria; c\_\_Actinobacteria; o\_\_Actinomycetales; f\_\_Propionibacteriaceae | susceptible | - -Looking down the list of taxa, we can see that three of the seven are -from the *Firmicutes* phylum, in which the organisms are generally -characterized by a Gram-positive cell wall structure. Vancomycin’s -mechanism of action is to disrupt construction of the cell wall in -Gram-positive organisms, so we would generally predict that organisms in -this phylum would be susceptible to the antibiotic. Likewise, the -*Actinobacteria* are Gram-positive, so the final lineage is predicted to -be susceptible. The three remaining lineages are Gram-negative organisms -from the *Proteobacteria*, and are predicted to be resistant. - -Now, if you’ve read the Wikipedia article on vancomycin, you might know -that most species of *Lactobacillus* are naturally resistant to the -drug, although they are Gram-positive bacteria in the *Firmicutes* -phylum. Here, we don’t have an assignment to the *Lactobacillus* genus, -but instead to the *Lactobacillaceae* family, so the prediction stands -as susceptible. - -## Databases for bacterial phenotypes and antibiotic susceptibility - -The `mirix` package comes with two built-in databases. The -`taxon_phenotypes` database contains information on Gram-stain and -aerobic status for over 900 bacterial taxa. The taxa were selected to -cover many taxa encountered in the human microbiome. It is here where we -note that the *Firmicutes* are generally Gram-positive. - -``` r -taxon_phenotypes %>% - filter(taxon %in% "Firmicutes") -#> taxon rank aerobic_status gram_stain doi -#> 1 Firmicutes Phylum Gram-positive 10.1099/00207713-28-1-1 -``` - -The second database `taxon_susceptibility`, contains information about -bacterial susceptibility to specific antibiotics. It is here, for -example, where we note that *Lactobacillus* species are typically -resistant to vancomycin. - -``` r -taxon_susceptibility %>% - filter(taxon %in% "Lactobacillus") -#> taxon rank antibiotic value doi -#> 1 Lactobacillus Genus vancomycin resistant 10.1128/AEM.01738-18 -``` - -If you need to add or modify information in these databases, you can -copy the data frames to new variables, make the changes you’d like, and -pass the new databases directly to the `mirix_vancomycin()` or -`antibiotic_susceptibility_vancomycin()` functions. - -## Predicting taxon abundances for a given value of the index - -In addition to calculating the antibiotics index for a given sample, we -can predict what the abundances in a sample might look like at a given -value of the index. Our approach is to re-balance the total abundances -of resistant and susceptible bacteria in the sample, while preserving -the relative abundances within the resistant taxa and within the -susceptible taxa. Our method will also preserve the total abundance of -each sample, in case the total abundance is not equal to 1. For taxa -that are not annotated as either resistant or susceptible, we don’t -change the abundance at all. - -We’ll use a healthy control sample, `Healthy.6`, to demonstrate. First, -we’ll calculate the susceptibility to vancomycin for each lineage. - -``` r -healthy6_data <- weiss2021_data %>% - filter(sample_id %in% "Healthy.6") %>% - mutate(taxon = word(lineage, -1)) %>% - mutate(taxon = fct_reorder(taxon, proportion)) %>% - mutate(susceptibility = antibiotic_susceptibility_vancomycin(lineage)) -``` - -Above, we also made a shorter label for the taxa and sorted the values -based on proportion in the sample, to aid in plotting. Here is a chart -of the taxon abundances and their susceptibility. - -``` r -healthy6_data %>% - ggplot(aes(x = proportion, y = taxon, shape = susceptibility)) + - geom_point() + - scale_x_log10() + - scale_shape_manual(values = c(1, 19), na.value = 3) -``` - -![](tools/readme/weiss_healthy6-1.png) - -Most taxa in the sample are annotated as susceptible to vancomycin, -including the most abundant taxon, *Ruminococcaceae*. One taxon, RF39, -is not annotated. Only a few taxa are annotated as resistant to -vancomycin, thus it’s not surprising that the vancomycin index for the -sample is negative. - -``` r -healthy6_data %>% - summarise(vanc = mirix_vancomycin(proportion, lineage)) -#> # A tibble: 1 × 1 -#> vanc -#> -#> 1 -0.207 -``` - -How would we expect the proportions to change if the index increased to -a positive value, say 0.5? We can use `predict_abundance()` to run the -calculation. - -``` r -healthy6_data %>% - mutate(predicted = predict_abundance(0.5, proportion, susceptibility)) %>% - rename(observed = proportion) %>% - pivot_longer( - c(observed, predicted), names_to = "method", values_to = "abundance") %>% - ggplot(aes(x = abundance, y = taxon, color = method, shape = susceptibility)) + - geom_point() + - scale_x_log10() + - scale_shape_manual(values = c(1, 19), na.value = 3) + - scale_color_brewer(palette = "Paired") -``` - -![](tools/readme/weiss_healthy6_prediction-1.png) - -Here, we can see that the abundances have increased for the resistant -taxa, such as *Bacteroides* (near the top) and *Enterobacteriaceae* (at -the bottom). For susceptible taxa, the abundances have decreased. For -the taxon that’s not annotated, RF39 (near the middle), the abundance -has not changed at all. - -To finish, let’s re-calculate the vancomycin index for our predicted -abundances, so we can verify that it has the expected value of 0.5. - -``` r -healthy6_data %>% - mutate(predicted = predict_abundance(0.5, proportion, susceptibility)) %>% - summarise(vanc = mirix_vancomycin(predicted, lineage)) -#> # A tibble: 1 × 1 -#> vanc -#> -#> 1 0.500 -``` + + + +# mirix + + + +[![R-CMD-check](https://github.com/PennChopMicrobiomeProgram/mirix/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/PennChopMicrobiomeProgram/mirix/actions/workflows/R-CMD-check.yaml) +[![codecov](https://codecov.io/gh/PennChopMicrobiomeProgram/mirix/graph/badge.svg?token=7DBBaNoGDc)](https://codecov.io/gh/PennChopMicrobiomeProgram/mirix) + + +The goal of mirix is to calculate the Microbiome Response Index (MiRIx) +for a given bacterial community. Often this will be used to predict the +community’s susceptibility to an antibiotic. + +## Installation + +You can install the development version of mirix with `devtools`: + +``` r +#install.packages("devtools") +devtools::install_github("PennChopMicrobiomeProgram/mirix") +``` + +## Calculating antibiotic index values + +Here, we’ll load the `mirix` package, demonstrate some basic tasks, and +give some pointers for its use. Although we could accomplish all our +tasks in base R, the `mirix` package works very nicely with functions +from the tidyverse. We’ll import those functions now. + +``` r +library(tidyverse) +``` + +Next, we’ll load the `mirix` library. + +``` r +library(mirix) +``` + +This package comes with a built-in data set, `weiss2021_data`, from a +study of the gut microbiota in children with sepsis (PMID 33786436). The +children in this study were exposed to a range of antibiotics, and fecal +samples were collected across a series of time windows after diagnosis +(`study_window` A-E). Bacterial communities in the fecal samples were +profiled by sequencing the 16S rRNA gene, which serves as a fingerprint +to identify bacteria in each sample. The study included samples from a +set of healthy children in a similar age group for comparison. Here is a +summary of the number of samples in each time window: + +``` r +weiss2021_data %>% + distinct(sample_id, study_group, study_window) %>% + count(study_group, study_window) %>% + knitr::kable() +``` + +| study_group | study_window | n | +|:------------|:-------------|----:| +| Healthy | NA | 44 | +| Sepsis | A | 17 | +| Sepsis | B | 9 | +| Sepsis | C | 7 | +| Sepsis | D | 2 | +| Sepsis | E | 8 | + +for each sample collected, the data frame contains the relative +abundance of all bacteria with a proportion of more than 0.001. Here is +one of the sepsis samples, from subject 19019 in time window A. In this +sample, the sequencing results indicated the following types of +bacteria: + +``` r +weiss2021_data %>% + filter(sample_id %in% "Sepsis.19019.A") %>% + select(lineage, proportion) %>% + knitr::kable() +``` + +| lineage | proportion | +|:---------------------------------------------------------------------------------------------------------------------------------|-----------:| +| k\_\_Bacteria; p\_\_Firmicutes; c\_\_Bacilli; o\_\_Lactobacillales; f\_\_Enterococcaceae; g\_\_Enterococcus | 0.5491550 | +| k\_\_Bacteria; p\_\_Firmicutes; c\_\_Bacilli; o\_\_Lactobacillales; f\_\_Lactobacillaceae | 0.3418542 | +| k\_\_Bacteria; p\_\_Proteobacteria; c\_\_Gammaproteobacteria; o\_\_Pseudomonadales; f\_\_Pseudomonadaceae; g\_\_Pseudomonas | 0.0825587 | +| k\_\_Bacteria; p\_\_Proteobacteria; c\_\_Gammaproteobacteria; o\_\_Enterobacteriales; f\_\_Enterobacteriaceae | 0.0094255 | +| k\_\_Bacteria; p\_\_Proteobacteria; c\_\_Gammaproteobacteria; o\_\_Xanthomonadales; f\_\_Xanthomonadaceae; g\_\_Stenotrophomonas | 0.0069635 | +| k\_\_Bacteria; p\_\_Firmicutes; c\_\_Bacilli; o\_\_Bacillales; f\_\_Staphylococcaceae; g\_\_Staphylococcus | 0.0051231 | +| k\_\_Bacteria; p\_\_Actinobacteria; c\_\_Actinobacteria; o\_\_Actinomycetales; f\_\_Propionibacteriaceae | 0.0027708 | + +For each type of bacteria, the taxonomic assignment includes all the +taxon names from the kingdom on down to the most specific taxon that +could be determined from the sequence, in most cases the genus. +Following the [NCBI taxonomy +browser](https://www.ncbi.nlm.nih.gov/taxonomy), we call this result the +lineage. + +Our goal will be to use the lineage information to predict which +bacteria in each sample would be susceptible or resistant to various +antibiotics. For a given antibiotic, we construct an +*antibiotic-specific* Mircrobiome Response Index by taking the log-ratio +of the abundance for resistant organisms over that of susceptible +organisms. + +If the bacterial community is dominated by susceptible organisms, the +index will be negative. Conversely, the index is positive if susceptible +organisms constitute a minority. If an antibiotic has the predicted +effect on a bacterial community, the index should increase after the +antibiotic is introduced. + +Let’s compute the vancomycin response index for each sample in the +study. + +``` r +weiss2021_vanc <- weiss2021_data %>% + group_by(sample_id, study_group, study_window) %>% + summarise(vanc = mirix_vancomycin(proportion, lineage), .groups = "drop") + +weiss2021_vanc %>% + ggplot(aes(x=study_window, y = vanc)) + + geom_boxplot() + + facet_grid(~ study_group, scales = "free_x", space = "free_x") + + labs(x = "Study window", y = "Vancomycin-specific index") +``` + +![](tools/readme/weiss_vancomycin_index-1.png) + +For healthy children, the medain value of the index is about 0.2, +whereas it is roughly 0.85 across the samples from children with sepsis. +Let’s look further into how the index was calculated, and check out +which bacteria were labeled as susceptible or resistant to vancomycin. + +## Susceptible and resistant bacteria + +The `mirix` library offers some lower-level functions that show more +details about how the index was calculated. For each antibiotic with an +index function, there is an accompanying function to determine the +susceptibility for each lineage. Let’s list out the susceptibility for +the lineages in the sample from subject 19019: + +``` r +weiss2021_data %>% + filter(sample_id %in% "Sepsis.19019.A") %>% + mutate(susceptibility = antibiotic_susceptibility_vancomycin(lineage)) %>% + select(lineage, susceptibility) %>% + knitr::kable() +``` + +| lineage | susceptibility | +|:---------------------------------------------------------------------------------------------------------------------------------|:---------------| +| k\_\_Bacteria; p\_\_Firmicutes; c\_\_Bacilli; o\_\_Lactobacillales; f\_\_Enterococcaceae; g\_\_Enterococcus | susceptible | +| k\_\_Bacteria; p\_\_Firmicutes; c\_\_Bacilli; o\_\_Lactobacillales; f\_\_Lactobacillaceae | susceptible | +| k\_\_Bacteria; p\_\_Proteobacteria; c\_\_Gammaproteobacteria; o\_\_Pseudomonadales; f\_\_Pseudomonadaceae; g\_\_Pseudomonas | resistant | +| k\_\_Bacteria; p\_\_Proteobacteria; c\_\_Gammaproteobacteria; o\_\_Enterobacteriales; f\_\_Enterobacteriaceae | resistant | +| k\_\_Bacteria; p\_\_Proteobacteria; c\_\_Gammaproteobacteria; o\_\_Xanthomonadales; f\_\_Xanthomonadaceae; g\_\_Stenotrophomonas | resistant | +| k\_\_Bacteria; p\_\_Firmicutes; c\_\_Bacilli; o\_\_Bacillales; f\_\_Staphylococcaceae; g\_\_Staphylococcus | susceptible | +| k\_\_Bacteria; p\_\_Actinobacteria; c\_\_Actinobacteria; o\_\_Actinomycetales; f\_\_Propionibacteriaceae | susceptible | + +Looking down the list of taxa, we can see that three of the seven are +from the *Firmicutes* phylum, in which the organisms are generally +characterized by a Gram-positive cell wall structure. Vancomycin’s +mechanism of action is to disrupt construction of the cell wall in +Gram-positive organisms, so we would generally predict that organisms in +this phylum would be susceptible to the antibiotic. Likewise, the +*Actinobacteria* are Gram-positive, so the final lineage is predicted to +be susceptible. The three remaining lineages are Gram-negative organisms +from the *Proteobacteria*, and are predicted to be resistant. + +Now, if you’ve read the Wikipedia article on vancomycin, you might know +that most species of *Lactobacillus* are naturally resistant to the +drug, although they are Gram-positive bacteria in the *Firmicutes* +phylum. Here, we don’t have an assignment to the *Lactobacillus* genus, +but instead to the *Lactobacillaceae* family, so the prediction stands +as susceptible. + +## Databases for bacterial phenotypes and antibiotic susceptibility + +The `mirix` package comes with two built-in databases. The +`taxon_phenotypes` database contains information on Gram-stain and +aerobic status for over 900 bacterial taxa. The taxa were selected to +cover many taxa encountered in the human microbiome. It is here where we +note that the *Firmicutes* are generally Gram-positive. + +``` r +whatbacteria::taxon_phenotypes %>% + filter(taxon %in% "Firmicutes") +#> taxon rank aerobic_status gram_stain doi +#> 1 Firmicutes Phylum Gram-positive 10.1099/00207713-28-1-1 +``` + +The second database `taxon_susceptibility`, contains information about +bacterial susceptibility to specific antibiotics. It is here, for +example, where we note that *Lactobacillus* species are typically +resistant to vancomycin. + +``` r +whatbacteria::taxon_susceptibility %>% + filter(taxon %in% "Lactobacillus") +#> taxon rank antibiotic value doi +#> 1 Lactobacillus Genus vancomycin resistant 10.1128/AEM.01738-18 +``` + +If you need to add or modify information in these databases, you can +copy the data frames to new variables, make the changes you’d like, and +pass the new databases directly to the `mirix_vancomycin()` or +`antibiotic_susceptibility_vancomycin()` functions. + +## Predicting taxon abundances for a given value of the index + +In addition to calculating the antibiotics index for a given sample, we +can predict what the abundances in a sample might look like at a given +value of the index. Our approach is to re-balance the total abundances +of resistant and susceptible bacteria in the sample, while preserving +the relative abundances within the resistant taxa and within the +susceptible taxa. Our method will also preserve the total abundance of +each sample, in case the total abundance is not equal to 1. For taxa +that are not annotated as either resistant or susceptible, we don’t +change the abundance at all. + +We’ll use a healthy control sample, `Healthy.6`, to demonstrate. First, +we’ll calculate the susceptibility to vancomycin for each lineage. + +``` r +healthy6_data <- weiss2021_data %>% + filter(sample_id %in% "Healthy.6") %>% + mutate(taxon = word(lineage, -1)) %>% + mutate(taxon = fct_reorder(taxon, proportion)) %>% + mutate(susceptibility = antibiotic_susceptibility_vancomycin(lineage)) +``` + +Above, we also made a shorter label for the taxa and sorted the values +based on proportion in the sample, to aid in plotting. Here is a chart +of the taxon abundances and their susceptibility. + +``` r +healthy6_data %>% + ggplot(aes(x = proportion, y = taxon, shape = susceptibility)) + + geom_point() + + scale_x_log10() + + scale_shape_manual(values = c(1, 19), na.value = 3) +``` + +![](tools/readme/weiss_healthy6-1.png) + +Most taxa in the sample are annotated as susceptible to vancomycin, +including the most abundant taxon, *Ruminococcaceae*. One taxon, RF39, +is not annotated. Only a few taxa are annotated as resistant to +vancomycin, thus it’s not surprising that the vancomycin index for the +sample is negative. + +``` r +healthy6_data %>% + summarise(vanc = mirix_vancomycin(proportion, lineage)) +#> # A tibble: 1 × 1 +#> vanc +#> +#> 1 0.207 +``` + +How would we expect the proportions to change if the index increased to +a positive value, say 0.5? We can use `predict_abundance()` to run the +calculation. + +``` r +healthy6_data %>% + mutate(predicted = predict_abundance(0.5, proportion, susceptibility)) %>% + rename(observed = proportion) %>% + pivot_longer( + c(observed, predicted), names_to = "method", values_to = "abundance") %>% + ggplot(aes(x = abundance, y = taxon, color = method, shape = susceptibility)) + + geom_point() + + scale_x_log10() + + scale_shape_manual(values = c(1, 19), na.value = 3) + + scale_color_brewer(palette = "Paired") +``` + +![](tools/readme/weiss_healthy6_prediction-1.png) + +Here, we can see that the abundances have increased for the resistant +taxa, such as *Bacteroides* (near the top) and *Enterobacteriaceae* (at +the bottom). For susceptible taxa, the abundances have decreased. For +the taxon that’s not annotated, RF39 (near the middle), the abundance +has not changed at all. + +To finish, let’s re-calculate the vancomycin index for our predicted +abundances, so we can verify that it has the expected value of 0.5. + +``` r +healthy6_data %>% + mutate(predicted = predict_abundance(0.5, proportion, susceptibility)) %>% + summarise(vanc = mirix_vancomycin(predicted, lineage)) +#> # A tibble: 1 × 1 +#> vanc +#> +#> 1 0.50 +``` diff --git a/appveyor.yml b/appveyor.yml deleted file mode 100644 index 8c6621c..0000000 --- a/appveyor.yml +++ /dev/null @@ -1,51 +0,0 @@ -# DO NOT CHANGE the "init" and "install" sections below - -# Download script file from GitHub -init: - ps: | - $ErrorActionPreference = "Stop" - Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1" - Import-Module '..\appveyor-tool.ps1' -install: - ps: Bootstrap - -cache: - - C:\RLibrary - -environment: - NOT_CRAN: true - # env vars that may need to be set, at least temporarily, from time to time - # see https://github.com/krlmlr/r-appveyor#readme for details - # USE_RTOOLS: true - # R_REMOTES_STANDALONE: true - -# Adapt as necessary starting from here - -build_script: - - travis-tool.sh install_deps - -test_script: - - travis-tool.sh run_tests - -on_failure: - - 7z a failure.zip *.Rcheck\* - - appveyor PushArtifact failure.zip - -artifacts: - - path: '*.Rcheck\**\*.log' - name: Logs - - - path: '*.Rcheck\**\*.out' - name: Logs - - - path: '*.Rcheck\**\*.fail' - name: Logs - - - path: '*.Rcheck\**\*.Rout' - name: Logs - - - path: '\*_*.tar.gz' - name: Bits - - - path: '\*_*.zip' - name: Bits diff --git a/codecov.yml b/codecov.yml deleted file mode 100644 index 04c5585..0000000 --- a/codecov.yml +++ /dev/null @@ -1,14 +0,0 @@ -comment: false - -coverage: - status: - project: - default: - target: auto - threshold: 1% - informational: true - patch: - default: - target: auto - threshold: 1% - informational: true diff --git a/data-raw/Lactobacillus_data.csv b/data-raw/Lactobacillus_data.csv deleted file mode 100644 index c8b1aa4..0000000 --- a/data-raw/Lactobacillus_data.csv +++ /dev/null @@ -1,199 +0,0 @@ -name,Growth conditions,rank,doi,vancomycin -Lactobacillus algidus,Anaerobic,Species,10.1128/AEM.01738-18,TRUE -Lactobacillus ceti,Strictly anaerobic,Species,10.1128/AEM.01738-18,TRUE -Lactobacillus composti,Microaerophilic,Species,10.1128/AEM.01738-18,TRUE -Lactobacillus delbrueckii subsp. bulgaricus,Microaerophilic,Species,10.1128/AEM.01738-18,TRUE -Lactobacillus delbrueckii subsp. delbrueckii,Microaerophilic,Species,10.1128/AEM.01738-18,TRUE -Lactobacillus delbrueckii subsp. indicus,Microaerophilic,Species,10.1128/AEM.01738-18,TRUE -Lactobacillus delbrueckii subsp. jakobsenii,Anaerobic,Species,10.1128/AEM.01738-18,TRUE -Lactobacillus delbrueckii subsp. lactis,Microaerophilic,Species,10.1128/AEM.01738-18,TRUE -Lactobacillus farciminis,Microaerophilic,Species,10.1128/AEM.01738-18,TRUE -Lactobacillus hilgardii,Preferably anaerobic,Species,10.1128/AEM.01738-18,TRUE -Lactobacillus pobuzihii,Microaerophilic,Species,10.1128/AEM.01738-18,TRUE -Lactobacillus sanfranciscensis,Anaerobic,Species,10.1128/AEM.01738-18,TRUE -Lactobacillus acetotolerans,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus acidifarinae,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus acidipiscis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus acidophilus,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus agilis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus alimentarius,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus amylolyticus,Preferably anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus amylophilus,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus amylotrophicus,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus amylovorus,Microaerophilic-anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus animalis,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus antri,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus apinorum,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus apis,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus apodemi,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus aquaticus,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus aviarius subsp. araffinosus,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus aviarius subsp. aviarius,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus backii,Preferably anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus bifermentans,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus bombi,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus bombicola,Strictly anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus brantae,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus brevis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus buchneri,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus cacaonum,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus camelliae,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacilllus capillatus,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus casei,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus colehominis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus collinoides,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus concavus,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus coryniformis subsp. coryniformis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus coryniformis subsp. torquens,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus crispatus,Preferably anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus crustorum,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus curieae,Facultatively anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus curvatus,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus dextrinicus,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus diolivorans,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus equi,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus equicursoris,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus equigenerosi,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus fabifermentans,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus faecis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus farraginis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus fermentum,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus floricola,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus florum,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus formosensis,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus fornicalis,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus fructivorans,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus frumenti,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus fuchuensis,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus furfuricola,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus futsaii,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus gallinarum,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus gasseri,Preferably anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus gastricus,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus ghanensis,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus gigeriorum,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus ginsenosidimutans,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus gorillae,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus graminis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus hammesii,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus hamsteri,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus harbinensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus hayakitensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus heilongjiangensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus helsingborgensis,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus helveticus,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus herbarum,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus hokkaidonensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus hominis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus homohiochii,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus hordei,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus iners,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus ingluviei,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus insicii,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus intestinalis,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus iwatensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus jensenii,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus johnsonii,Preferably anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus kalixensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus kefiranofaciens subsp. kefiranofaciens,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus kefiranofaciens subsp. kefirgranum,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus kefiri,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus kimbladii,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus kimchicus,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus kimchiensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus kisonensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacilus kitasatonis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus koreensis,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus kullabergensis,Strictly anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus kunkeei,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus lindneri,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus malefermentans,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus mali,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus manihotivorans,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus mellifer,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus mellis,Strictly anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus melliventris,Strictly anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus mindensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus mixtipabuli,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus modestisalitolerans,Facultatively anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus mucosae,Preferably anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus mudanjiangensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus murinus,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus nagelii,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus namurensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus nantensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus nasuensis,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus nenjiangensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus nodensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus odoratitofui,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus oeni,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus oligofermentans,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus oris,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus oryzae,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus otakiensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus ozensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus panis,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus pantheris,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus parabrevis,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus parabuchneri,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus paracasei subsp. paracasei,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus paracasei subsp. tolerans,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus paracollinoides,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus parafarraginis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus parakefiri,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus paralimentarius,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus paraplantarum,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus pasteurii,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus paucivorans,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus pentosus,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus perolens,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus plajomi,Facultatively anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus plantarum,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus plantarum subsp. argentoratensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus pontis,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus porcinae,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus psittaci,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus rapi,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus rennini,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus reuteri,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus rhamnosus,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus rodentium,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus rossiae,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus ruminis,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus saerimneri,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus sakei subsp. carnosus,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus sakei subsp. sakei,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus salivarius,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus saniviri,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus satsumensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus secaliphilus,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus selangorensis,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus senioris,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus senmaizukei,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus sharpeae,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus shenzhenensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus sicerae,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus silagei,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus siliginis,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus similis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus songhuajiangensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus spicheri,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus sucicola,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus suebicus,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus sunkii,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus taiwanensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus thailandensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus tucceti,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus ultunensis,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus uvarum,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus vaccinostercus,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus vaginalis,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus versmoldensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus vespulae,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus vini,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus wasatchensis,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus xiangfangensis,Aerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus yonginensis,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus zeae,Anaerobic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus zymae,Microaerophilic,Species,10.1128/AEM.01738-18,FALSE -Lactobacillus arizonensis,Aerobic,Species,10.1128/AEM.01738-18,FALSE \ No newline at end of file diff --git a/data-raw/genera_0831.txt b/data-raw/genera_0831.txt deleted file mode 100644 index 4fc8a81..0000000 --- a/data-raw/genera_0831.txt +++ /dev/null @@ -1,208 +0,0 @@ -name doi aerobic_status morphology motility spore_formation gram_stain bile_sensitive saccharolytic comments -Bacteroides 10.1099/00207713-39-1-85 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic -Prevotella 10.1099/00207713-40-2-205 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic -Akkermansia 10.1099/ijs.0.02873-0 obligate anaerobe oval-shaped/ coccobaccili non-motile not indicated Gram-negative not indicated saccharolytic -Anaerostripes 10.1078/0723-2020-00096 obligate anaerobe rod/ bacilli not indicated non-spore forming Gram-positive not indicated saccharolytic -Anaerotruncas 10.1099/ijs.0.02653-0 facultative anaerobe rod/ bacilli not indicated non-spore forming Gram-positive not indicated saccharolytic -Barnesiella 10.1099/ijs.0.64709-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic -Blautia 10.1099/ijs.0.65208-0 obligate anaerobe cocci or oval-shaped non-motile mixed Gram-positive not indicated saccharolytic -Roseburia 10.1099/00207713-33-3-618 obligate anaerobe slightly curved rods motile non-spore forming Gram-negative not indicated saccharolytic -Alloprevotella 10.1099/ijs.0.041376-0 obligate anaerobe rod/ bacilli non-motile not indicated Gram-negative not indicated saccharolytic -Porphyromonas 10.1099/00207713-38-1-128 obligate anaerobe rods or oval-shaped non-motile non-spore forming Gram-negative not indicated asaccharolytic -Paraprevotella 10.1099/ijs.0.008169-0 obligate anaerobe not indicated non-motile non-spore forming Gram-negative not indicated saccharolytic -Parabacteroides 10.1099/ijs.0.64192-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic -Oscillibacter 10.1099/ijs.0.64717-0 obligate anaerobe rods or slightly curved rods motile non-spore forming Gram-negative not indicated saccharolytic -Odoribacter 10.1099/ijs.0.63458-0 anaerobe (unspecified) fusiform non-motile non-spore forming Gram-negative not indicated not indicated -Faecalibacterium 10.1099/00207713-52-6-2141 obligate anaerobe not indicated non-motile non-spore forming Gram-negative not indicated saccharolytic -Enterobacter 10.1099/0096266X-10-2-71 facultative anaerobe rod/ bacilli variable not indicated Gram-negative not indicated saccharolytic -Shuttleworthia 10.1099/00207713-52-5-1469 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive no growth in 20% bile saccharolytic -Sediminibacterium 10.1099/ijs.0.65514-0 obligate anaerobe rod/ bacilli not indicated not indicated Gram-negative not indicated not indicated -Peptoniphilus 10.1099/00207713-51-4-1521 obligate anaerobe cocci non-motile non-spore forming Gram-positive not indicated asaccharolytic -Moryella 10.1099/ijs.0.64705-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-variable not indicated saccharolytic -Holdemania 10.1099/00207713-47-4-1201 obligate anaerobe rod/ bacilli not indicated non-spore forming Gram-positive not indicated saccharolytic -Gordonibacter 10.1099/ijs.0.005900-0 obligate anaerobe oval-shaped/ coccobaccili motile non-spore forming Gram-positive not indicated asaccharolytic -Dorea 10.1099/00207713-52-2-423 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic -Sutterella 10.1099/00207713-46-1-252 microaerobe or anaerobe rod/ bacilli not indicated not indicated Gram-negative no growth in 20% bile asaccharolytic -Sporobacter 10.1099/00207713-46-2-512 obligate anaerobe rod/ bacilli not indicated spore forming Gram-positive not indicated not indicated -Pseudoflavonifractor 10.1099/ijs.0.016725-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated not indicated -Flavonifractor 10.1099/ijs.0.016725-0 obligate anaerobe rod/ bacilli variable mixed Gram-variable not indicated asaccharolytic -Achromobacter 10.1099/00207713-31-4-477 aerobe rod/ bacilli motile non-spore forming Gram-negative not indicated asaccharolytic -Aerococcus 10.1099/00221287-8-3-475 facultative anaerobe cocci non-motile not indicated Gram-positive growth in 20% bile mixed -Catenibacterium 10.1099/00207713-50-4-1595 obligate anaerobe not indicated non-motile non-spore forming Gram-positive not indicated saccharolytic -Collinsella 10.1099/00207713-49-2-557 obligate anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic -Aggregatibacter 10.1099/ijs.0.64207-0 facultative anaerobe rods or oval-shaped non-motile not indicated Gram-negative not indicated saccharolytic -Anaerococcus 10.1099/00207713-51-4-1521 obligate anaerobe cocci non-motile not indicated Gram-positive not indicated mixed -Succinivibrio N/A anaerobe (unspecified) slightly curved rods motile non-spore forming Gram-negative not indicated saccharolytic http://jb.asm.org/content/72/1/22.full.pdf -Lachnospira N/A anaerobe (unspecified) slightly curved rods motile non-spore forming Gram-positive not indicated saccharolytic http://jb.asm.org/content/72/1/22.full.pdf -Parasutterella 10.1099/ijs.0.002519-0 obligate anaerobe cocci or oval-shaped non-motile non-spore forming Gram-negative growth in 20% bile asaccharolytic -Paralactobacillus 10.1099/00207713-50-1-19 not indicated rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic -Oribacterium 10.1099/ijs.0.63060-0 obligate anaerobe ovoid motile non-spore forming Gram-positive not indicated saccharolytic -Ochrobactrum 10.1099/00207713-38-4-406 obligate anaerobe rod/ bacilli motile not indicated Gram-negative not indicated saccharolytic -Murdochiella 10.1099/ijs.0.015909-0 obligate anaerobe cocci non-motile not indicated Gram-positive no growth in 20% bile asaccharolytic -Mogibacterium 10.1099/00207713-50-2-679 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated asaccharolytic -Megasphaera 10.1099/00207713-21-2-187 obligate anaerobe cocci non-motile non-spore forming Gram-negative not indicated saccharolytic -Hallella 10.1099/00207713-44-2-187 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic -Johnsonella 10.1099/00207713-44-2-187 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated asaccharolytic -Granulicatella 10.1099/00207713-50-1-365 facultative anaerobe pleomorphic non-motile non-spore forming Gram-positive not indicated saccharolytic -Gemmiger 10.1099/00207713-25-2-202 obligate anaerobe not indicated not indicated not indicated Gram-variable not indicated saccharolytic -Gardnerella 10.1099/00207713-30-1-170 facultative anaerobe rod/ bacilli not indicated not indicated Gram-variable not indicated saccharolytic -Facklamia 10.1099/00207713-47-3-880 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated asaccharolytic -Enterococcus 10.1099/00207713-34-1-31 facultative anaerobe ovoid variable non-spore forming Gram-positive not indicated saccharolytic -Dialister 10.1099/00207713-44-2-187 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated asaccharolytic -Delftia 10.1099/00207713-49-2-567 obligate anaerobe rods or slightly curved rods motile non-spore forming Gram-negative not indicated asaccharolytic -Cronobacter 10.1099/ijs.0.65577-0 facultative anaerobe rod/ bacilli motile not indicated Gram-negative not indicated saccharolytic -Citrobacter N/A not indicated rod/ bacilli not indicated non-spore forming Gram-negative not indicated saccharolytic http://jb.asm.org/content/23/2/167.full.pdf -Chryseobacterium 10.1099/00207713-44-4-827 aerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic -Centipeda 10.1099/00207713-33-3-628 anaerobe (unspecified) rod/ bacilli motile non-spore forming Gram-negative not indicated saccharolytic -Butyricicoccus 10.1099/ijs.0.65730-0 obligate anaerobe cocci non-motile not indicated Gram-positive not indicated not indicated -Bulleidia 10.1099/00207713-50-3-979 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive no growth in 20% bile saccharolytic -Brevundimonas 10.1099/00207713-44-3-499 aerobe rod/ bacilli motile not indicated Gram-negative not indicated asaccharolytic -Anaeroglobus 10.1099/00207713-52-3-983 obligate anaerobe cocci or oval-shaped non-motile non-spore forming Gram-negative not indicated saccharolytic -Arthrobacter 10.1099/00207713-45-4-837 aerobe not indicated variable non-spore forming Gram-positive not indicated not indicated -Atopobium 10.1099/ijs.0.065243-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated -Bacillus 10.1099/ijs.0.64993-0 aerobe rod/ bacilli non-motile not indicated Gram-variable not indicated not indicated -Butyricimonas 10.1099/ijs.0.007674-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic -Deinococcus 10.1099/00207713-31-3-353 aerobe oval-shaped/ coccobaccili non-motile not indicated Gram-positive not indicated not indicated -Helicobacter 10.1099/00207713-39-4-397 microaerobe or anaerobe not indicated motile not indicated Gram-negative not indicated not indicated -Microbacterium 10.1099/00207713-48-3-739 aerobe rod/ bacilli variable not indicated Gram-positive not indicated not indicated -Pseudobutyrivibrio 10.1099/00207713-46-2-559 anaerobe (unspecified) rod/ bacilli not indicated non-spore forming Gram-negative not indicated not indicated -Schwartzia 10.1099/00207713-47-1-155 anaerobe (unspecified) slightly curved rods motile non-spore forming Gram-negative not indicated asaccharolytic -Succiniclasticum 10.1099/00207713-45-2-297 not indicated rods or slightly curved rods non-motile non-spore forming Gram-negative not indicated not indicated -Tannerella 10.1099/00207713-52-3-841 anaerobe (unspecified) not indicated non-motile not indicated Gram-negative no growth in 20% bile not indicated -Alistipes 10.1099/ijs.0.014571-0 anaerobe (unspecified) "rods, cocci, or oval-shaped" non-motile not indicated Gram-negative not indicated not indicated -Catonella 10.1099/00207713-44-2-187 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated not indicated -Kingella 10.1099/00207713-26-4-447 aerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated not indicated -Eremococcus 10.1099/00207713-49-4-1381 facultative anaerobe cocci not indicated not indicated Gram-positive not indicated saccharolytic -Variovorax 10.1099/00207713-41-3-445 aerobe rods or slightly curved rods motile not indicated not indicated not indicated saccharolytic -Slackia 10.1099/00207713-49-2-595 obligate anaerobe "rods, cocci, or oval-shaped" non-motile non-spore forming Gram-positive no growth in 20% bile asaccharolytic -Pyramidobacter 10.1099/ijs.0.000364-0 obligate anaerobe rod/ bacilli non-motile not indicated not indicated not indicated asaccharolytic -Abiotrophia 10.1099/00207713-45-4-798 facultative anaerobe "rods, cocci, or oval-shaped" non-motile non-spore forming Gram-positive not indicated not indicated -Bordetella 10.1099/00207713-51-4-1257 not indicated oval-shaped/ coccobaccili not indicated not indicated Gram-negative not indicated asaccharolytic aerobic status is not an option -Parascardovia 10.1099/00207713-52-3-809 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic -Olsenella 10.1099/00207713-51-5-1797 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated -Jonquetella 10.1099/ijs.0.65213-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated not indicated -Xylanibacter 10.1099/ijs.0.64364-0 not indicated rod/ bacilli non-motile non-spore forming Gram-negative not indicated not indicated -Eikenella 10.1099/00207713-22-2-73 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated asaccharolytic -Christensenella 10.1099/ijs.0.026989-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic -Acidaminococcus N/A anaerobe (unspecified) cocci or oval-shaped not indicated non-spore forming Gram-negative not indicated mixed http://jb.asm.org/content/98/2/756.full.pdf+html -Oribaculum 10.1099/00207713-44-2-187 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic -Cellulosimicrobium 10.1099/00207713-51-3-1007 facultative anaerobe slightly curved rods non-motile non-spore forming Gram-positive not indicated not indicated -Enterorhabdus 10.1099/ijs.0.003087-0 not indicated rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated -Anarosalibacter 10.1099/ijs.0.036566-0 obligate anaerobe rod/ bacilli motile spore forming Gram-positive not indicated not indicated -Murimonas 10.1099/ijs.0.000030 obligate anaerobe oval-shaped/ coccobaccili non-motile non-spore forming Gram-positive not indicated not indicated -Terrisporobacter 10.1099/ijs.0.059543-0 anaerobe (unspecified) rods or slightly curved rods motile spore forming Gram-variable not indicated not indicated -Intestinimonas 10.1099/ijs.0.051441-0 obligate anaerobe not indicated non-motile spore forming Gram-positive not indicated saccharolytic -Stenotrophomonas 10.1099/00207713-43-3-606 not indicated not indicated motile non-spore forming Gram-negative not indicated not indicated -Aminobacter 10.1099/00207713-42-1-84 not indicated rod/ bacilli motile non-spore forming Gram-negative not indicated asaccharolytic -Bradyrhizobium 10.1099/00207713-32-1-136 aerobe rod/ bacilli motile non-spore forming Gram-negative not indicated not indicated -Curvibacter 10.1099/ijs.0.02975-0 not indicated slightly curved rods variable not indicated Gram-negative not indicated not indicated -Herbaspirillum 10.1099/00207713-36-1-86 microaerobe or anaerobe slightly curved rods motile not indicated Gram-negative not indicated not indicated -Turicibacter 10.1099/00207713-52-4-1263 anaerobe (unspecified) rod/ bacilli not indicated non-spore forming Gram-positive not indicated not indicated -Rothia 10.1099/00207713-17-1-79 microaerobe or aerobe rods or cocci non-motile non-spore forming not indicated not indicated saccharolytic -Pedobacter 10.1099/00207713-48-1-165 obligate anaerobe rod/ bacilli variable not indicated Gram-negative not indicated saccharolytic -Parvibacter 10.1099/ijs.0.045344-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated -Acidovorax 10.1099/00207713-40-4-384 aerobe rods or slightly curved rods motile not indicated Gram-negative not indicated not indicated -Aeromicrobium 10.1099/00207713-41-3-363 aerobe rods or cocci non-motile non-spore forming Gram-positive not indicated not indicated -Afipia 10.1099/00207713-52-5-1773 not indicated rod/ bacilli motile not indicated Gram-negative not indicated not indicated -Aquabacterium 10.1099/00207713-49-2-769 microaerobe rod/ bacilli motile not indicated Gram-negative not indicated not indicated -Aurantimonas 10.1099/ijs.0.02359-0 obligate anaerobe not indicated not indicated non-spore forming Gram-negative not indicated not indicated -Azoarcus 10.1099/00207713-43-3-574 not indicated rods or slightly curved rods motile not indicated Gram-negative not indicated not indicated -Xanthomonas 10.1099/00207713-40-4-348 aerobe rods or slightly curved rods variable not indicated Gram-negative not indicated not indicated -Papillibacter 10.1099/00207713-50-3-1221 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated -Lachnobacterium 10.1099/00207713-51-6-1977 obligate anaerobe rod/ bacilli not indicated non-spore forming Gram-positive not indicated not indicated -Azospira 10.1099/00207713-50-2-649 microaerobe slightly curved rods motile non-spore forming Gram-negative not indicated saccharolytic -Beutenbergia 10.1099/00207713-49-4-1733 microaerobe or aerobe rods or cocci non-motile non-spore forming Gram-positive not indicated not indicated -Micrococcus 10.1099/00207713-45-4-682 aerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated -Polaromonas 10.1099/00207713-46-3-822 aerobe rod/ bacilli motile not indicated Gram-negative not indicated not indicated -Pseudoxanthomonas 10.1099/00207713-50-1-273 aerobe rod/ bacilli not indicated not indicated Gram-negative not indicated not indicated -Psychrobacter 10.1099/00207713-36-3-388 aerobe oval-shaped/ coccobaccili non-motile non-spore forming Gram-negative not indicated not indicated -Sphingobium 10.1099/00207713-51-4-1405 aerobe rod/ bacilli variable non-spore forming Gram-negative not indicated asaccharolytic -Sphingomonas 10.1099/00207713-51-4-1405 aerobe rod/ bacilli variable non-spore forming Gram-negative not indicated asaccharolytic -Sphingopyxis 10.1099/00207713-51-4-1405 aerobe rod/ bacilli variable non-spore forming Gram-positive not indicated not indicated -Sulfuritalea 10.1099/ijs.0.024968-0 facultative anaerobe slightly curved rods motile non-spore forming Gram-negative not indicated not indicated -Tsukamurella 10.1099/00207713-38-4-385 aerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated -Undibacterium 10.1099/ijs.0.64785-0 not indicated rod/ bacilli non-motile non-spore forming Gram-negative not indicated not indicated -Bosea 10.1099/00207713-46-4-981 aerobe rod/ bacilli not indicated not indicated Gram-negative not indicated not indicated -Brevibacillus 10.1099/00207713-46-4-939 aerobe rod/ bacilli motile spore forming Gram-variable not indicated not indicated -Caulobacter 10.1099/00207713-49-2-483 not indicated not indicated motile not indicated Gram-negative not indicated not indicated -Comamonas 10.1099/00207713-35-4-443 aerobe rods or slightly curved rods motile non-spore forming Gram-negative not indicated not indicated -Craurococcus 10.1099/00207713-48-3-1043 aerobe cocci non-motile not indicated Gram-negative not indicated not indicated -Cupriavidus 10.1099/ijs.0.63247-0 not indicated rod/ bacilli motile not indicated Gram-negative not indicated not indicated -Devosia 10.1099/00207713-46-1-16 aerobe rod/ bacilli motile non-spore forming Gram-negative not indicated not indicated -Dietzia 10.1099/00207713-45-1-32 aerobe rods or cocci not indicated non-spore forming Gram-positive not indicated not indicated -Duganella 10.1099/00207713-47-4- aerobe rod/ bacilli motile non-spore forming Gram-negative not indicated not indicated -Dyadobacter 10.1099/00207713-50-2-751 aerobe rods or cocci non-motile not indicated Gram-negative not indicated not indicated -Enhydrobacter 10.1099/00207713-37-3-289 facultative anaerobe rods or cocci not indicated not indicated Gram-negative not indicated not indicated -Hoeflea 10.1099/ijs.0.63291-0 aerobe rod/ bacilli motile non-spore forming Gram-negative not indicated not indicated -Hydrotalea 10.1099/ijs.0.023002-0 aerobe rod/ bacilli non-motile not indicated Gram-negative not indicated not indicated -Janthinobacterium 10.1099/00207713-49-4-1577 aerobe rod/ bacilli motile not indicated Gram-negative not indicated not indicated -Kocuria 10.1099/00207713-45-4-682 aerobe cocci not indicated non-spore forming Gram-positive not indicated not indicated -Limnobacter 10.1099/00207713-51-4-1463 obligate anaerobe slightly curved rods motile non-spore forming Gram-negative not indicated asaccharolytic -Mesorhizobium 10.1099/00207713-47-3-895 aerobe rod/ bacilli motile non-spore forming Gram-negative not indicated saccharolytic -Methylophilus 10.1099/00207713-37-4-446 aerobe rods or slightly curved rods variable non-spore forming Gram-negative not indicated saccharolytic -Methyloversatilis 10.1099/ijs.0.64422-0 not indicated rod/ bacilli non-motile not indicated Gram-negative not indicated not indicated -Microlunatus 10.1099/00207713-45-1-17 aerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated -Niastella 10.1099/ijs.0.64242-0 aerobe not indicated motile not indicated Gram-negative not indicated not indicated -Novosphingobium 10.1099/00207713-51-4-1405 obligate anaerobe rod/ bacilli variable non-spore forming Gram-negative not indicated not indicated -Olivibacter 10.1099/ijs.0.64561-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated not indicated -Paracoccus 10.1099/00207713-19-4-375 obligate anaerobe cocci non-motile non-spore forming Gram-negative not indicated asaccharolytic -Patulibacter 10.1099/ijs.0.63796-0 aerobe rod/ bacilli not indicated non-spore forming Gram-positive not indicated not indicated -Wautersiella 10.1099/ijs.0.64393-0 not indicated rod/ bacilli non-motile not indicated Gram-negative not indicated not indicated -Actinobaculum 10.1099/00207713-47-3-899 facultative anaerobe rods or slightly curved rods non-motile non-spore forming Gram-positive not indicated saccharolytic -Anaerotruncus 10.1099/ijs.0.02653-0 obligate anaerobe rod/ bacilli not indicated non-spore forming Gram-positive not indicated saccharolytic -Propionimicrobium 10.1099/00207713-52-6-1925 anaerobe (unspecified) cocci non-motile non-spore forming Gram-positive somewhat inhibited by 20% bile saccharolytic -Granulicella 10.1099/ijs.0.021824-0 aerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated not indicated -Mobiluncus 10.1099/00207713-34-2-177 anaerobe (unspecified) slightly curved rods motile non-spore forming Gram-variable not indicated saccharolytic -Fusibacter 10.1099/00207713-49-3-1141 obligate anaerobe fusiform motile non-spore forming Gram-positive not indicated not indicated -Alkaliphilus 10.1099/00207713-51-4-1245 anaerobe (unspecified) rods or slightly curved rods motile spore forming Gram-positive not indicated not indicated -Acetivibrio 10.1099/00207713-30-1-179 anaerobe (unspecified) rods or slightly curved rods motile non-spore forming Gram-negative not indicated not indicated -Caloramator 10.1099/00207713-44-4-812 obligate anaerobe rod/ bacilli not indicated spore forming Gram-negative not indicated saccharolytic -Caloranaerobacter 10.1099/00207713-51-5-1789 anaerobe (unspecified) rod/ bacilli motile non-spore forming Gram-negative not indicated saccharolytic -Caminicella 10.1099/00207713-52-5-1621 anaerobe (unspecified) rod/ bacilli motile spore forming Gram-negative not indicated not indicated -Cellulosibacter 10.1099/ijs.0.027854-0 obligate anaerobe rods or slightly curved rods motile spore forming Gram-positive not indicated not indicated -Garciella 10.1099/ijs.0.02662-0 obligate anaerobe rod/ bacilli motile spore forming Gram-positive not indicated not indicated -Guggenheimella 10.1099/ijs.0.63116-0 obligate anaerobe rods or cocci non-motile non-spore forming Gram-positive not indicated asaccharolytic -Hespellia 10.1099/ijs.0.02719-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic -Oxobacter 10.1099/00207713-44-4-812 obligate anaerobe rod/ bacilli not indicated spore forming Gram-positive not indicated not indicated -Soehngenia 10.1099/ijs.0.02668-0 anaerobe (unspecified) rod/ bacilli motile spore forming Gram-positive not indicated saccharolytic -Tepidibacter 10.1099/ijs.0.02600-0 anaerobe (unspecified) rod/ bacilli motile spore forming Gram-positive not indicated not indicated -Clostridium 10.1002/9781118960608.gbm00619 anaerobe (unspecified) rod/ bacilli variable mixed Gram-variable not indicated mixed -Corynebacterium 10.1002/9781118960608.gbm00026 facultative anaerobe rods or slightly curved rods non-motile non-spore forming Gram-positive not indicated mixed -Tepidimicrobium 10.1099/ijs.0.63694-0 anaerobe (unspecified) rod/ bacilli motile non-spore forming Gram-positive not indicated not indicated -Desulfotomaculum N/A obligate anaerobe rods or slightly curved rods motile spore forming Gram-negative not indicated not indicated http://mmbr.asm.org/content/29/3/359.full.pdf+html -Thermincola 10.1099/ijs.0.63299-0 anaerobe (unspecified) rod/ bacilli motile non-spore forming Gram-positive not indicated not indicated -Thermohalobacter 10.1099/00207713-50-2-559 obligate anaerobe rod/ bacilli motile non-spore forming Gram-negative not indicated not indicated -Thermoterrabacterium 10.1099/00207713-47-2-541 anaerobe (unspecified) rod/ bacilli motile non-spore forming Gram-positive not indicated not indicated -Desulfosporosinus 10.1099/00207713-47-4-1134 obligate anaerobe slightly curved rods motile non-spore forming Gram-negative not indicated saccharolytic -Pelotomaculum 10.1099/00207713-52-5-1729 obligate anaerobe slightly curved rods non-motile spore forming Gram-variable not indicated not indicated -Lachnoanaerobaculum 10.1099/ijs.0.033613-0 obligate anaerobe rod/ bacilli not indicated spore forming Gram-variable not indicated saccharolytic -Helcococcus 10.1099/00207713-43-3-425 facultative anaerobe cocci non-motile not indicated Gram-positive no growth in 20% bile saccharolytic -Stomatobaculum 10.1099/ijs.0.042812-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-variable not indicated saccharolytic -Abyssivirga 10.1099/ijsem.0.000934 obligate anaerobe rods or cocci motile non-spore forming not indicated not indicated saccharolytic -Cellulosilyticum 10.1099/ijs.0.014712-0 anaerobe (unspecified) rods or slightly curved rods not indicated spore forming not indicated not indicated not indicated -Filifactor 10.1099/00207713-44-4-812 not indicated rod/ bacilli not indicated spore forming Gram-variable not indicated saccharolytic -Mobilitalea 10.1099/ijs.0.057109-0 obligate anaerobe rod/ bacilli motile spore forming Gram-positive not indicated not indicated -Pelospora 10.1099/00207713-50-2-645 obligate anaerobe not indicated not indicated spore forming not indicated not indicated not indicated -Pseudoramibacter 10.1099/00207713-46-4-1083 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic -Robinsoniella 10.1099/ijs.0.65676-0 anaerobe (unspecified) rods or oval-shaped not indicated spore forming Gram-positive not indicated saccharolytic -Sporobacterium 10.1099/00207713-49-4-1741 obligate anaerobe slightly curved rods motile spore forming Gram-positive not indicated asaccharolytic -Syntrophothermus 10.1099/00207713-50-2-771 obligate anaerobe slightly curved rods motile not indicated Gram-negative not indicated not indicated -Thermosyntropha 10.1099/00207713-46-4-1131 obligate anaerobe rod/ bacilli not indicated not indicated Gram-variable not indicated not indicated -Tissierella 10.1099/00207713-36-3-461 obligate anaerobe rod/ bacilli not indicated non-spore forming Gram-negative not indicated mixed -Eggerthella 10.1002/9781118960608.gbm00219 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated -Eubacterium 10.1002/9781118960608.gbm00629 obligate anaerobe pleomorphic rods variable non-spore forming Gram-positive not indicated mixed -Fusobacterium 10.1002/9781118960608.gbm00768 obligate anaerobe rod/ bacilli not indicated non-spore forming Gram-negative not indicated saccharolytic -Gemella 10.1002/9781118960608.gbm00578 facultative anaerobe ovoid non-motile non-spore forming Gram-variable no growth in 20% bile saccharolytic -Escherichia 10.1002/9781118960608.gbm01147 facultative anaerobe rod/ bacilli variable not indicated Gram-negative not indicated saccharolytic -Lactobacillus 10.1002/9781118960608.gbm00604 facultative anaerobe rods or oval-shaped variable non-spore forming Gram-positive not indicated saccharolytic -Lactococcus 10.1002/9781118960608.gbm00610 facultative anaerobe cocci or oval-shaped non-motile non-spore forming Gram-positive not indicated saccharolytic -Leptotrichia 10.1002/9781118960608.gbm00771 variable rods or slightly curved rods non-motile not indicated Gram-negative not indicated saccharolytic -Neisseria 10.1002/9781118960608.gbm00981 aerobe rods or cocci variable non-spore forming Gram-negative not indicated mixed -Propionibacterium 10.1002/9781118960608.gbm00167 microaerobe or anaerobe pleomorphic rods non-motile non-spore forming Gram-positive not indicated saccharolytic -Pseudomonas 10.1002/9781118960608.gbm01210 variable rods or slightly curved rods variable not indicated Gram-negative not indicated mixed -Ralstonia 10.1002/9781118960608.gbm00941 aerobe rod/ bacilli variable not indicated Gram-negative not indicated not indicated -Ruminococcus 10.1002/9781118960608.gbm00678 obligate anaerobe cocci variable not indicated Gram-positive not indicated saccharolytic -Sneathia 10.1002/9781118960608.gbm00773 anaerobe (unspecified) rod/ bacilli non-motile not indicated Gram-negative not indicated saccharolytic -Veillonella 10.1002/9781118960608.gbm00710 anaerobe (unspecified) cocci non-motile non-spore forming Gram-negative not indicated mixed -Staphylococcus 10.1002/9781118960608.gbm00569 facultative anaerobe cocci non-motile not indicated Gram-positive not indicated saccharolytic -Streptococcus 10.1002/9781118960608.gbm00612 facultative anaerobe cocci or ovoid non-motile non-spore forming Gram-positive not indicated saccharolytic \ No newline at end of file diff --git a/data-raw/phenotype_misc.csv b/data-raw/phenotype_misc.csv deleted file mode 100644 index 992b7b2..0000000 --- a/data-raw/phenotype_misc.csv +++ /dev/null @@ -1,18 +0,0 @@ -taxon,rank,aerobic_status,gram_stain,doi -Actinobacteria,Phylum,NA,Gram-positive,10.1128/MMBR.00019-15 -Bacteroidetes,Phylum,NA,Gram-negative,NA -Firmicutes,Phylum,NA,Gram-positive,10.1099/00207713-28-1-1 -Proteobacteria,Phylum,NA,Gram-negative,NA -Negativicutes,Class,NA,Gram-negative,10.4056/sigs.2981345 -Clostridia,Class,obligate anaerobe,Gram-positive,NA -Bacilli,Class,facultative anaerobe,Gram-positive,NA -Bacteroidales,Order,obligate anaerobe,Gram-negative,10.1128/microbiolspec.dmih2-0015-2015 -Rikenellaceae,Family,obligate anaerobe,Gram-negative,NA -Enterobacteriaceae,Family,facultative anaerobe,Gram-negative,NA -Haemophilus,Genus,facultative anaerobe,Gram-negative,10.1002/9781118960608.gbm01198 -Peptostreptococcus,Genus,obligate anaerobe,Gram-positive,10.1128/microbiolspec.dmih2-0015-2015 -Finegoldia,Genus,obligate anaerobe,Gram-positive,10.1128/microbiolspec.dmih2-0015-2015 -Parvimonas,Genus,obligate anaerobe,Gram-positive,10.1128/microbiolspec.dmih2-0015-2015 -Bifidobacterium,Genus,obligate anaerobe,Gram-positive,10.1128/microbiolspec.dmih2-0015-2015 -Salmonella,Genus,facultative anaerobe,Gram-negative,10.1002/9781118960608.gbm01166 -Listeria,Genus,facultative anaerobe,Gram-positive,10.1002/9781118960608.gbm00547 diff --git a/data-raw/species_0831.txt b/data-raw/species_0831.txt deleted file mode 100644 index f511263..0000000 --- a/data-raw/species_0831.txt +++ /dev/null @@ -1,798 +0,0 @@ -name doi aerobic_status morphology motility spore_formation gram_stain bile_sensitive saccharolytic comments urease catalase formate_production acetate_production propionate_production butyrate_production isobutyrate_production valerate_production isovalerate_production -Bacteroides vulgatus N/A not indicated oval-shaped/ coccobaccili non-motile not indicated Gram-negative not indicated saccharolytic http://jb.asm.org/content/25/4/389.full.pdf+html not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Aggregatibacter actinomycetemcomitans 10.1099/ijs.0.64207-0 not indicated rod/ bacilli not indicated not indicated not indicated not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium dentium 10.1099/00207713-24-1-6 anaerobe (unspecified) rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Corynebacterium kroppenstedtii 10.1099/00207713-48-4-1449 facultative anaerobe not indicated non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Gardnerella vaginalis 10.1099/00207713-30-1-170 facultative anaerobe pleomorphic non-motile not indicated Gram-variable not indicated saccharolytic urease negative not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Lactobacillus acidophilus 10.1099/00207713-20-3-325 not indicated rod/ bacilli not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus iners 10.1099/00207713-49-1-217 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus jensenii 10.1099/00221287-62-2-219 not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic not indicated not indicated not producted not producted not producted not producted not producted not producted not producted -Lactobacillus rhamnosus 10.1099/00207713-39-2-105 not indicated rod/ bacilli non-motile not indicated not indicated not indicated saccharolytic urease negative not indicated not producted not producted not producted not producted not producted not producted not producted -Aerococcus christensenii 10.1099/00207713-49-3-1125 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated urease negative catalase negative not indicated not producted not indicated not indicated not indicated not indicated not indicated -Akkermansia muciniphila 10.1099/ijs.0.02873-0 anaerobe (unspecified) oval-shaped/ coccobaccili non-motile not indicated Gram-negative not indicated not indicated not indicated not indicated not indicated not producted not indicated not producted not indicated not indicated not indicated -Achromobacter xylosoxidans 10.1099/00207713-31-4-477 obligate anaerobe rod/ bacilli motile non-spore forming Gram-negative not indicated asaccharolytic urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Brevundimonas diminuta 10.1099/00207713-44-3-499 aerobe rod/ bacilli motile not indicated Gram-negative not indicated not indicated not indicated not indicated not indicated consumed consumed consumed not indicated consumed minor product -Tannerella forsythia 10.1099/00207713-52-3-841 obligate anaerobe fusiform non-motile not indicated Gram-negative not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Sutterella wadsworthensis 10.1099/00207713-46-1-252 not indicated rod/ bacilli not indicated not indicated Gram-negative not indicated not indicated urease negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Brevundimonas vesicularis 10.1099/00207713-44-3-499 aerobe rod/ bacilli motile not indicated Gram-negative not indicated not indicated not indicated not indicated not indicated consumed not indicated consumed not indicated not producted not producted -Succinivibrio dextrinosolvens N/A anaerobe (unspecified) slightly curved rods not indicated non-spore forming Gram-negative not indicated saccharolytic http://jb.asm.org/content/72/1/22.full.pdf+html not indicated not indicated major product major product not indicated not indicated not indicated not indicated not indicated -Butyricicoccus pullicaecorum 10.1099/ijs.0.65730-0 anaerobe (unspecified) ovoid non-motile not indicated Gram-positive not indicated not indicated urease positive not indicated not indicated consumed not indicated major product not indicated not indicated not indicated -Succiniclasticum ruminis 10.1099/00207713-45-2-297 not indicated rods or slightly curved rods non-motile non-spore forming Gram-negative not indicated asaccharolytic urease negative catalase negative not producted not producted major product not producted not producted not producted not producted -Sporobacter termitidis 10.1099/00207713-46-2-512 obligate anaerobe slightly curved rods motile spore forming Gram-positive not indicated asaccharolytic not indicated not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Butyricimonas synergistica 10.1099/ijs.0.007674-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated minor product minor product major product minor product not indicated not indicated -Butyricimonas virosa 10.1099/ijs.0.007674-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase positive not indicated minor product minor product major product major product not indicated not indicated -Shuttleworthia satelles 10.1099/00207713-52-5-1469 obligate anaerobe slightly curved rods non-motile non-spore forming Gram-positive no growth in 20% bile saccharolytic not indicated catalase negative not indicated major product not indicated major product not indicated not indicated not indicated -Catenibacterium mitsuokai 10.1099/00207713-50-4-1595 obligate anaerobe not indicated non-motile non-spore forming Gram-positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Centipeda periodontii 10.1099/00207713-33-3-628 not indicated rod/ bacilli variable not indicated Gram-negative not indicated not indicated not indicated not indicated not indicated major product major product not indicated not indicated not indicated not indicated -Sediminibacterium salmoneum 10.1099/ijs.0.65514-0 aerobe rod/ bacilli motile not indicated Gram-negative not indicated saccharolytic urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Schwartzia succinivorans 10.1099/00207713-47-1-155 not indicated slightly curved rods motile not indicated not indicated not indicated asaccharolytic urease negative catalase negative not producted not producted major product not producted not producted not producted not producted -Roseburia cecicola 10.1099/00207713-33-3-618 obligate anaerobe slightly curved rods motile non-spore forming Gram-negative not indicated saccharolytic not indicated catalase negative not indicated consumed not indicated major product not indicated not indicated not indicated -Pseudoflavonifractor capillosus 10.1099/ijs.0.016725-0 obligate anaerobe rods or slightly curved rods non-motile non-spore forming Gram-negative no growth in 20% bile asaccharolytic not indicated not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Pseudobutyrivibrio ruminis 10.1099/00207713-46-2-559 not indicated slightly curved rods motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated major product minor product not indicated major product not indicated not indicated not indicated -Eremococcus coleocola 10.1099/00207713-49-4-1381 facultative anaerobe cocci not indicated not indicated Gram-positive not indicated saccharolytic urease variable catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Porphyromonas asaccharolytica 10.1099/00207713-38-1-128 obligate anaerobe rods or oval-shaped non-motile non-spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated major product minor product major product minor product not indicated minor product -Peptoniphilus asaccharolyticus 10.1099/00207713-51-4-1521 not indicated not indicated not indicated not indicated not indicated not indicated asaccharolytic urease negative not indicated not indicated not indicated not indicated major product not indicated not indicated not indicated -Parasutterella excrementihominis 10.1099/ijs.0.002519-0 obligate anaerobe cocci or oval-shaped non-motile non-spore forming Gram-negative growth in 20% bile asaccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Paraprevotella clara 0.1099/ijs.0.008169-0 obligate anaerobe not indicated non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Paralactobacillus selangorensis 10.1099/00207713-50-1-19 not indicated rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Parabacteroides distasonis 10.1099/ijs.0.64192-0 not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Oscillibacter valericigenes 10.1099/ijs.0.64717-0 obligate anaerobe slightly curved rods motile non-spore forming Gram-negative not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated major product not indicated -Oribacterium sinus 10.1099/ijs.0.63060-0 obligate anaerobe ovoid motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Odoribacter denticanis 10.1099/ijs.0.63458-0 anaerobe (unspecified) fusiform non-motile non-spore forming Gram-negative not indicated not indicated not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Ochrobactrum anthropi 10.1099/00207713-38-4-406 not indicated not indicated motile not indicated not indicated not indicated saccharolytic not indicated catalase positive not indicated consumed consumed not indicated consumed not indicated not indicated -Porphyromonas gingivalis 10.1099/00207713-38-1-128 obligate anaerobe rods or oval-shaped non-motile non-spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated major product minor product major product minor product not indicated minor product -Variovorax paradoxus 10.1099/00207713-41-3-445 aerobe rods or slightly curved rods motile not indicated not indicated not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Pyramidobacter piscolens 10.1099/ijs.0.000364-0 obligate anaerobe rod/ bacilli non-motile not indicated Gram-negative no growth in 20% bile asaccharolytic not indicated catalase negative not indicated major product minor product not indicated minor product not indicated minor product -Barnesiella viscericola 10.1099/ijs.0.64709-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Dorea formicigenerans 10.1099/00207713-52-2-423 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated not indicated not indicated major product major product not producted not indicated not indicated not indicated not indicated -Dorea longicatena 10.1099/00207713-52-2-423 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-variable not indicated not indicated not indicated catalase negative major product major product not indicated not indicated not indicated not indicated not indicated -Facklamia hominis 10.1099/00207713-47-3-880 facultative anaerobe ovoid non-motile non-spore forming Gram-positive not indicated not indicated urease variable catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Flavonifractor plautii 10.1099/ijs.0.016725-0 anaerobe (unspecified) rod/ bacilli variable mixed Gram-variable not indicated asaccharolytic not indicated not indicated not indicated major product not indicated major product not indicated not indicated not indicated -Bordetella petrii 10.1099/00207713-51-4-1257 microaerobe or anaerobe rods or oval-shaped non-motile non-spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Olsenella uli 10.1099/00207713-51-5-1797 anaerobe (unspecified) rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Jonquetella antrhopi 10.1099/ijs.0.65213-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated not indicated not indicated catalase negative not indicated major product major product not indicated minor product not indicated major product -Prevotella amnii 10.1099/ijs.0.65118-0 anaerobe (unspecified) rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Xylanibacter oryzae 10.1099/ijs.0.64364-0 not indicated rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile not indicated urease negative catalase negative not indicated major product major product not indicated not indicated not indicated not indicated -Erysipelothrix tonsillarum 10.1099/00207713-37-2-166 not indicated rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Eikenella corrodens 10.1099/00207713-22-2-73 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated asaccharolytic urease negative catalase negative not producted not producted not producted not producted not producted not producted not producted -Christensenella minuta 10.1099/ijs.0.026989-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated major product not indicated major product not indicated not indicated not indicated -Murdochiella asaccharolytica 10.1099/ijs.0.015909-0 obligate anaerobe cocci non-motile not indicated Gram-positive no growth in 20% bile asaccharolytic urease negative catalase negative not indicated minor product not indicated minor product not indicated not indicated not indicated -Moryella indoligenes 10.1099/ijs.0.64705-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-variable not indicated saccharolytic urease negative catalase negative not indicated major product not indicated major product not indicated not indicated not indicated -Mogibacterium pumilum 10.1099/00207713-50-2-679 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Mogibacterium vescum 10.1099/00207713-50-2-679 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Megasphaera micronuciformis 10.1099/ijs.0.02378-0 obligate anaerobe cocci non-motile not indicated Gram-negative not indicated not indicated not indicated catalase negative not indicated major product major product major product not indicated not indicated major product -Holdemania filiformis 10.1099/00207713-47-4- anaerobe (unspecified) rod/ bacilli not indicated non-spore forming Gram-positive not indicated not indicated not indicated catalase negative minor product major product not indicated not indicated not indicated not indicated not indicated -Helicobacter pylori 10.1099/00207713-39-4-397 aerobe slightly curved rods motile not indicated Gram-negative not indicated not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helicobacter mustelae 10.1099/00207713-39-4-397 microaerobe or anaerobe slightly curved rods motile not indicated Gram-negative not indicated not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Granulicatella adiacens 10.1099/00207713-50-1-365 facultative anaerobe rods, cocci, or oval-shaped non-motile non-spore forming Gram-positive not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Granulicatella elegans 10.1099/00207713-50-1-365 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Granulicatella balaenopterae 10.1099/00207713-50-1-365 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated urease positive catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lachnospira multipara N/A not indicated slightly curved rods motile not indicated Gram-variable not indicated saccharolytic http://jb.asm.org/content/72/1/22.full.pdf+html not indicated catalase negative major product major product not indicated not indicated not indicated not indicated not indicated -Gordonibacter pamelaeae 10.1099/ijs.0.005900-0 obligate anaerobe oval-shaped/ coccobaccili motile non-spore forming Gram-positive not indicated not indicated not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Anaerococcus prevotii 10.1099/00207713-51-4-1521 not indicated not indicated not indicated not indicated not indicated not indicated mixed urease variable not indicated not indicated not indicated not indicated major product not indicated not indicated not indicated -Anaeroglobus geminatus 10.1099/00207713-52-3-983 obligate anaerobe cocci or oval-shaped not indicated non-spore forming Gram-negative not indicated mixed not indicated catalase negative not indicated major product major product major product major product not indicated major product -Bulleidia extructa 10.1099/00207713-50-3-979 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive no growth in 20% bile saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Acidaminococcus fermentans N/A anaerobe (unspecified) cocci or oval-shaped not indicated non-spore forming Gram-negative not indicated mixed http://jb.asm.org/content/98/2/756.full.pdf+html not indicated not indicated not indicated major product not producted major product not indicated not indicated not indicated -Johnsonella ignava 10.1099/00207713-44-2-187 anaerobe (unspecified) rod/ bacilli not indicated not indicated Gram-negative no growth in 20% bile asaccharolytic not indicated catalase negative not indicated major product not indicated minor product minor product not indicated major product -Hallella seregens 10.1099/00207713-44-2-187 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Catonella morbi 10.1099/00207713-44-2-187 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated minor product major product not indicated not indicated not indicated not indicated not indicated -Dialister pneumosintes 10.1099/00207713-44-2-187 anaerobe (unspecified) rod/ bacilli not indicated non-spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated minor product minor product not indicated not indicated not indicated not indicated -Oribaculum catoniae 10.1099/00207713-44-2-187 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated minor product major product major product not indicated not indicated not indicated minor product -Arthrobacter agilis 10.1099/00207713-45-4- aerobe ovoid variable non-spore forming Gram-positive not indicated not indicated urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Collinsella aerofaciens 10.1099/00207713-49-2-557 obligate anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Delftia acidovorans 10.1099/00207713-49-2-567 obligate anaerobe slightly curved rods motile non-spore forming Gram-negative not indicated not indicated not indicated catalase positive not indicated consumed not indicated consumed consumed consumed consumed -Atopobium deltae 10.1099/ijs.0.065243-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated urease negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Enterorhabdus mucosicola 10.1099/ijs.0.003087-0 not indicated rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Kingella orale 10.1099/00207713-43-3-490 facultative anaerobe rods or oval-shaped non-motile not indicated Gram-negative not indicated not indicated urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Microbacterium immunditiarum 10.1099/ijs.0.033373-0 not indicated rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Alloprevotella tannerae 10.1099/ijs.0.041376-0 obligate anaerobe rod/ bacilli non-motile not indicated Gram-negative not indicated saccharolytic urease negative not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Alloprevotella rava 10.1099/ijs.0.041376-0 obligate anaerobe rod/ bacilli non-motile not indicated Gram-negative no growth in 20% bile saccharolytic urease negative not indicated not indicated major product not indicated not indicated not indicated not indicated minor product -Anaerostripes butyraticus 10.1099/ijs.0.015289-0 anaerobe (unspecified) rod/ bacilli non-motile spore forming Gram-positive not indicated not indicated urease negative not indicated not indicated consumed consumed major product not indicated not indicated not indicated -Campylobacter concisus 10.1099/00207713-31-4-432 microaerobe or anaerobe slightly curved rods motile non-spore forming Gram-negative not indicated not indicated urease negative catalase negative major product not indicated not indicated not indicated not indicated not indicated not indicated -Actinomyces bowdenii 10.1099/00207713-49-4-1873 facultative anaerobe rods or slightly curved rods non-motile not indicated Gram-positive not indicated saccharolytic not indicated catalase positive not indicated major product not indicated not indicated not indicated not indicated not indicated -Actinomyces timonensis 10.1099/ijs.0.012914-0 anaerobe (unspecified) rod/ bacilli not indicated not indicated Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Anaerococcus tetradius 10.1099/00207713-51-4-1521 not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic urease positive not indicated not indicated not indicated not indicated major product not indicated not indicated not indicated -Bacteroides acidifaciens 10.1099/00207713-50-1-145 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Bacteroides caecimuris N/A obligate anaerobe rod/ bacilli not indicated not indicated Gram-negative not indicated saccharolytic https://www.nature.com/articles/nmicrobiol2016131 not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides ovatus N/A not indicated oval-shaped/ coccobaccili not indicated not indicated not indicated not indicated saccharolytic http://jb.asm.org/content/25/4/389.full.pdf+html not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides xylanisolvens 10.1099/ijs.0.65504-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic urease negative catalase negative not indicated major product major product not indicated not indicated not indicated not indicated -Bifidobacterium animalis 10.1099/00207713-24-1-21 anaerobe (unspecified) rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product not producted not producted not indicated not indicated not indicated -Cellulosimicrobium cellulans 10.1099/00207713-51-3-1007 facultative anaerobe rods or cocci not indicated not indicated not indicated not indicated saccharolytic not indicated catalase positive minor product major product not indicated not indicated not indicated not indicated not indicated -Coprococcus eutactus 10.1099/00207713-24-2-260 obligate anaerobe cocci non-motile not indicated Gram-positive not indicated saccharolytic not indicated not indicated major product major product not producted major product not indicated not indicated not indicated -Anaerosalibacter bizertensis 10.1099/ijs.0.036566-0 obligate anaerobe rod/ bacilli motile spore forming Gram-positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacillus thermoamylovorans 0.1099/00207713-45-1-9 facultative anaerobe rod/ bacilli motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase positive major product major product not indicated not indicated not indicated not indicated not indicated -Enterococcus faecalis 10.1099/00207713-34-1-31 facultative anaerobe ovoid variable not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Enterococcus faecium 10.1099/00207713-34-1-31 not indicated ovoid variable not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Enterococcus gallinarum 10.1099/00207713-34-2-220 not indicated cocci non-motile not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Enterococcus hirae 10.1099/00207713-35-1-73 facultative anaerobe ovoid non-motile not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus warneri 10.1099/00207713-25-1-62 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus capitis 10.1099/00207713-25-1-62 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus hominis 10.1099/00207713-25-1-62 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus simulans 10.1099/00207713-25-1-62 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus xylosus 10.1099/00207713-25-1-50 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Murimonas intestini 10.1099/ijs.0.000030 obligate anaerobe oval-shaped/ coccobaccili non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Intestinimonas butyriciproducens 10.1099/ijs.0.051441-0 obligate anaerobe fusiform non-motile spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated major product not indicated major product not indicated not indicated not indicated -Stenotrophomonas maltophilia 10.1099/00207713-43-3-606 not indicated not indicated motile non-spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Enterorhabdus caecimuris 10.1099/ijs.0.015016-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Eubacterium hallii 10.1099/00207713-24-2-260 obligate anaerobe rod/ bacilli non-motile not indicated Gram-positive not indicated saccharolytic not indicated not indicated minor product major product not producted major product not indicated not indicated not indicated -Lactobacillus apodemi 10.1099/ijs.0.64147-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus johnsonii 10.1099/00207713-42-3-487 facultative anaerobe rod/ bacilli not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus rodentium 10.1099/ijs.0.054924-0 microaerobe or anaerobe rod/ bacilli not indicated not indicated Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus salivarius N/A not indicated rod/ bacilli not indicated non-spore forming Gram-positive not indicated saccharolytic http://jb.asm.org/content/65/6/681.full.pdf+html not indicated not indicated not producted not producted not producted not producted not producted not producted not producted -Lactobacillus taiwanensis 10.1099/ijs.0.006783-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not producted not producted not producted not producted not producted not producted not producted -Mycoplasma faucium 10.1099/00207713-24-2-252 not indicated pleomorphic not indicated not indicated Gram-negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Oceanobacillus caeni 10.1099/ijs.0.65335-0 aerobe rod/ bacilli motile spore forming Gram-positive not indicated saccharolytic urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Paenibacillus lactis 10.1099/ijs.0.02822-0 aerobe rods or slightly curved rods motile spore forming not indicated not indicated saccharolytic urease negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Parabacteroides goldsteinii 10.1099/ijs.0.64192-0 not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic urease negative not indicated minor product major product minor product not indicated not indicated not indicated minor product -Parabacteroides merdae 10.1099/ijs.0.64192-0 not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Parabacteroides johnsonii 10.1099/ijs.0.64588-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic urease negative catalase positive not indicated major product minor product not indicated not indicated not indicated minor product -Frisingicoccus caecimuris N/A obligate anaerobe cocci not indicated not indicated not indicated not indicated not indicated https://www.nature.com/articles/nmicrobiol2016131#Fig3 not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Aminobacter aminovorans 10.1099/00207713-42-1-84 not indicated rod/ bacilli motile non-spore forming Gram-negative not indicated asaccharolytic urease negative catalase positive not indicated consumed not indicated not indicated not indicated not indicated not indicated -Aminobacter aganoensis 10.1099/00207713-42-1-84 not indicated rod/ bacilli motile non-spore forming Gram-negative not indicated asaccharolytic urease negative catalase positive not indicated consumed not indicated not indicated not indicated not indicated not indicated -Blautia faecis 10.1099/ijs.0.036541-0 obligate anaerobe oval-shaped/ coccobaccili non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Bradyrhizobium japonicum 10.1099/00207713-32-1-136 not indicated rod/ bacilli motile non-spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Curvibacter gracilis 10.1099/ijs.0.02975-0 not indicated slightly curved rods variable not indicated Gram-negative not indicated not indicated not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Herbaspirillum seropedicae 10.1099/00207713-36-1-86 microaerobe or anaerobe slightly curved rods motile not indicated Gram-negative not indicated not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Oscillibacter ruminantium 10.1099/ijs.0.041749-0 obligate anaerobe rods or slightly curved rods motile non-spore forming Gram-negative not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Turicibacter sanguinis 10.1099/00207713-52-4-1263 obligate anaerobe rod/ bacilli not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus defectivus 10.1099/00207713-39-3-290 facultative anaerobe pleomorphic non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus adjacens 10.1099/00207713-39-3-290 facultative anaerobe pleomorphic non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Ruminococcus bromii 10.1099/00207713-22-2-78 obligate anaerobe cocci not indicated not indicated Gram-positive not indicated saccharolytic not indicated not indicated major product major product not indicated not indicated not indicated not indicated not indicated -Rothia aeria 10.1099/ijs.0.02828-0 aerobe cocci or oval-shaped not indicated not indicated Gram-positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Rothia nasimurium 10.1099/00207713-50-3-1247 facultative anaerobe cocci non-motile not indicated Gram-positive not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Pedobacter heparinus 10.1099/00207713-48-1-165 obligate anaerobe rod/ bacilli motile not indicated Gram-negative not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Parvibacter caecicola 10.1099/ijs.0.045344-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated urease negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Faecalibacterium prausnitzii 10.1099/00207713-52-6-2141 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated major product consumed not indicated major product not indicated not indicated not indicated -Acidovorax facilis 10.1099/00207713-40-4-384 aerobe rods or slightly curved rods motile not indicated Gram-negative not indicated not indicated urease variable not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Afipia felis 10.1099/00207713-52-5-1773 not indicated rod/ bacilli motile not indicated Gram-negative not indicated not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Aquabacterium commune 10.1099/00207713-49-2-769 microaerobe rod/ bacilli motile non-spore forming Gram-negative not indicated not indicated not indicated catalase negative not indicated major product not indicated major product not indicated major product not indicated -Aurantimonas coralicida 10.1099/ijs.0.02359-0 obligate anaerobe rod/ bacilli motile non-spore forming Gram-negative not indicated not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Azoarcus indigens 10.1099/00207713-43-3-574 not indicated rods or slightly curved rods motile not indicated Gram-negative not indicated not indicated urease variable catalase positive not indicated consumed consumed not indicated not indicated not indicated not indicated -Papillibacter cinnamivorans 10.1099/00207713-50-3-1221 anaerobe (unspecified) rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated not indicated not indicated not indicated not producted not indicated not producted not indicated not indicated not indicated -Lachnobacterium bovis 10.1099/00207713-51-6-1977 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated Rare motile cells have been observed in old cultures not indicated not indicated not indicated minor product not indicated minor product not indicated not indicated not indicated -Ruminococcus callidus 10.1099/00207713-24-2-260 obligate anaerobe cocci non-motile not indicated Gram-positive somewhat inhibited by 20% bile saccharolytic not indicated not indicated major product major product not indicated not indicated not indicated not indicated not indicated -Eubacterium desmolans 10.1099/00207713-36-2-183 obligate anaerobe rod/ bacilli motile non-spore forming Gram-positive no growth in 20% bile not indicated not indicated catalase negative not indicated major product not indicated major product not indicated not indicated not indicated -Ruminococcus champanellensis 10.1099/ijs.0.027375-0 obligate anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Clostridium cellulosi 10.1099/00207713-41-2-306 obligate anaerobe rods or slightly curved rods motile spore forming Gram-negative not indicated not indicated not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Ruminococcus gnavus 10.1099/00207713-26-2-238 obligate anaerobe cocci variable non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated major product major product not indicated not indicated not indicated not indicated not indicated -Clostridium orbiscindens 10.1099/00207713-41-3-355 obligate anaerobe rod/ bacilli motile spore forming Gram-variable not indicated not indicated urease negative not indicated not indicated major product minor product major product not indicated not indicated not indicated -Ruminococcus lactaris 10.1099/00207713-26-2-238 obligate anaerobe cocci or oval-shaped non-motile non-spore forming Gram-variable not indicated saccharolytic urease negative not indicated major product major product not indicated not indicated not indicated not indicated not indicated -Ruminococcus obeum 10.1099/00207713-26-2-238 obligate anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Ruminococcus productus 10.1099/00207713-44-1-130 obligate anaerobe cocci not indicated not indicated Gram-positive not indicated saccharolytic not indicated catalase negative major product major product not indicated not indicated not indicated not indicated not indicated -Anaerofilum agile 10.1099/00207713-46-4-871 obligate anaerobe rod/ bacilli motile non-spore forming Gram-positive not indicated not indicated not indicated catalase negative major product major product not producted not indicated minor product not indicated minor product -Roseburia faecis 10.1099/ijs.0.64098-0 not indicated slightly curved rods motile not indicated Gram-variable not indicated saccharolytic not indicated catalase negative major product consumed not indicated major product not indicated not indicated not indicated -Roseburia hominis 10.1099/ijs.0.64098-0 obligate anaerobe slightly curved rods motile not indicated Gram-variable not indicated saccharolytic not indicated catalase negative major product consumed not indicated major product not indicated not indicated not indicated -Roseburia inulinivorans 10.1099/ijs.0.64098-0 obligate anaerobe slightly curved rods motile not indicated Gram-variable not indicated saccharolytic not indicated catalase negative major product consumed not indicated major product not indicated not indicated not indicated -Azospira oryzae 10.1099/00207713-50-2-649 microaerobe slightly curved rods motile non-spore forming Gram-negative not indicated saccharolytic not indicated catalase positive not indicated consumed consumed not indicated not indicated not indicated consumed -Anaerofilum pentosovorans 10.1099/00207713-46-4-871 obligate anaerobe rod/ bacilli variable non-spore forming Gram-positive not indicated not indicated not indicated catalase negative minor product major product minor product minor product minor product not indicated minor product -Beutenbergia cavernae 10.1099/00207713-49-4-1733 microaerobe or aerobe rods or cocci non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Polaromonas vacuolata 10.1099/00207713-46-3-822 aerobe rod/ bacilli motile not indicated Gram-negative not indicated not indicated urease positive catalase positive not indicated consumed consumed consumed not indicated not indicated not indicated -Psychrobacter immobilis 10.1099/00207713-36-3-388 aerobe oval-shaped/ coccobaccili non-motile non-spore forming Gram-negative not indicated not indicated urease variable catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Sphingobium yanoikuyae 10.1099/00207713-51-4-1405 aerobe rod/ bacilli variable non-spore forming Gram-negative not indicated asaccharolytic urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Sphingopyxis macrogoltabida 10.1099/00207713-51-4-1405 aerobe rod/ bacilli variable non-spore forming Gram-positive not indicated not indicated not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Sulfuritalea hydrogenivorans 10.1099/ijs.0.024968-0 facultative anaerobe slightly curved rods motile non-spore forming Gram-negative not indicated not indicated not indicated catalase negative not indicated consumed not indicated consumed consumed not indicated not indicated -Tsukamurella paurometabolum 10.1099/00207713-38-4-385 aerobe rods or slightly curved rods non-motile non-spore forming Gram-positive not indicated not indicated not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Undibacterium pigrum 10.1099/ijs.0.64785-0 not indicated rod/ bacilli non-motile non-spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated consumed consumed not indicated not indicated not indicated not indicated -Staphylococcus agnetis 10.1099/ijs.0.028365-0 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus argensis 10.1099/ijs.0.000319 not indicated not indicated not indicated not indicated Gram-positive not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus argenteus 10.1099/ijs.0.062752-0 facultative anaerobe cocci not indicated not indicated Gram-positive not indicated not indicated urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus auricularis 10.1099/00207713-33-1-9 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus caprae 10.1099/00207713-33-3-480 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus carnosus 10.1099/00207713-32-2-153 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus caseolyticus 10.1099/00207713-32-1-15 aerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus cohnii 10.1099/00207713-25-1-50 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus condimenti 10.1099/00207713-48-3-651 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Escherichia albertii 10.1099/ijs.0.02475-0 not indicated rod/ bacilli non-motile not indicated Gram-negative not indicated not indicated urease negative catalase positive not indicated consumed not indicated not indicated not indicated not indicated not indicated -Escherichia marmotae 10.1099/ijs.0.000228 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated not indicated urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus delphini 10.1099/00207713-38-4-436 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus devriesei 10.1099/ijs.0.015982-0 not indicated cocci non-motile non-spore forming Gram-positive not indicated not indicated urease variable catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus felis 10.1099/00207713-39-4-373 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus fleurettii 10.1099/00207713-50-4-1521 aerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus australis 10.1099/00207713-51-4-1277 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus caballi 10.1099/ijs.0.65063-0 facultative anaerobe ovoid non-motile not indicated Gram-positive growth in 20% bile saccharolytic urease positive catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus henryi 10.1099/ijs.0.65063-0 anaerobe (unspecified) ovoid non-motile not indicated Gram-positive not indicated not indicated urease positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus canis 10.1099/00207713-36-3-422 facultative anaerobe cocci not indicated not indicated Gram-positive no growth in 20% bile saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus caprae 10.1099/ijsem.0.000697 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus castoreus 10.1099/ijs.0.63433-0 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus cecorum 10.1099/00207713-33-4-772 anaerobe (unspecified) cocci non-motile non-spore forming Gram-positive growth in 20% bile saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus constellatus 10.1099/00207713-24-2-260 anaerobe (unspecified) cocci or oval-shaped non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated major product major product not producted not indicated not indicated not indicated not indicated -Streptococcus criceti 10.1099/00207713-27-1-26 not indicated cocci not indicated not indicated Gram-positive not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus cristatus 10.1099/00207713-41-4-543 not indicated cocci not indicated not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus cuniculi 10.1099/ijs.0.063123-0 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus gallinarum 10.1099/00207713-33-3-480 microaerobe or anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus dentapri 10.1099/ijs.0.012799-0 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus dentasini 10.1099/ijs.0.047142-0 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus jettensis 10.1099/ijs.0.044438-0 not indicated cocci non-motile non-spore forming Gram-positive not indicated not indicated urease variable catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus dentirousetti 10.1099/ijs.0.65204-0 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus lugdunensis 10.1099/00207713-38-2-168 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated urease variable catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus dentisani 10.1099/ijs.0.054098-0 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus didelphis 10.1099/00207713-50-2-759 not indicated cocci not indicated not indicated Gram-positive not indicated not indicated not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus outrage 10.1099/00207713-47-3-724 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus downei 10.1099/00207713-38-1-25 not indicated cocci not indicated not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus massiliensis 10.1099/ijs.0.006486-0 aerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated urease negative catalase positive not indicated not producted not indicated not indicated not indicated not indicated not indicated -Streptococcus durans 10.1099/00207713-34-3-327 facultative anaerobe cocci not indicated not indicated Gram-positive growth in 20% bile saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus microti 10.1099/ijs.0.011429-0 not indicated cocci not indicated not indicated Gram-positive not indicated not indicated urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus muscae 10.1099/00207713-42-1-97 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus nepalensis 10.1099/ijs.0.02646-0 microaerobe or anaerobe cocci non-motile not indicated Gram-positive not indicated not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus pasteuri 10.1099/00207713-43-2-237 not indicated cocci non-motile non-spore forming Gram-positive not indicated not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus pettenkoferi 10.1099/ijs.0.64381-0 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Straphylococcus piscifermentans 10.1099/00207713-42-4-577 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus pseudintermedius 10.1099/ijs.0.63413-0 not indicated cocci not indicated not indicated Gram-positive not indicated not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus pulvereri 10.1099/00207713-45-1-169 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated urease variable catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus rostri 10.1099/ijs.0.012443-0 not indicated cocci non-motile not indicated Gram-positive not indicated not indicated urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus scheiferi 10.1099/00207713-38-2-168 not indicated cocci non-motile non-spore forming Gram-positive not indicated not indicated urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus schweitzeri 10.1099/ijs.0.062752-0 facultative anaerobe cocci not indicated not indicated Gram-positive not indicated not indicated urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus simiae 10.1099/ijs.0.63590-0 not indicated cocci non-motile non-spore forming Gram-positive not indicated not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus succinus 10.1099/00207713-48-2-511 not indicated cocci not indicated non-spore forming Gram-positive not indicated not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus vitulus 10.1099/00207713-44-3-454 microaerobe or anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bosea thiooxidans 10.1099/00207713-46-4-981 aerobe rod/ bacilli motile non-spore forming Gram-negative not indicated not indicated urease negative catalase positive not indicated consumed not indicated not indicated not indicated not indicated not indicated -Comamonas terrigena 10.1099/00207713-35-4-443 aerobe rods or slightly curved rods motile non-spore forming Gram-negative not indicated not indicated urease negative catalase positive not indicated consumed consumed consumed consumed consumed consumed -Craurococcus roseus 10.1099/00207713-48-3-1043 aerobe cocci motile not indicated Gram-negative not indicated not indicated not indicated catalase positive consumed consumed consumed consumed not indicated not indicated not indicated -Devosia riboflavina 10.1099/00207713-46-1-16 aerobe rod/ bacilli motile non-spore forming Gram-negative not indicated not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Dietzia maris 10.1099/00207713-45-1-32 aerobe rods or cocci not indicated non-spore forming Gram-positive not indicated not indicated not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Duganella zoogloeoides 10.1099/00207713-47-4- aerobe rod/ bacilli motile non-spore forming Gram-negative not indicated not indicated urease positive catalase positive not producted not producted not producted not producted not indicated not indicated not indicated -Dyadobacter fermentans 10.1099/00207713-50-2-751 aerobe rods or cocci non-motile not indicated Gram-negative not indicated not indicated not indicated catalase positive not indicated consumed not indicated not indicated not indicated not indicated not indicated -Enhydrobacter aerosaccus 10.1099/00207713-37-3-289 facultative anaerobe rod/ bacilli non-motile not indicated Gram-negative not indicated not indicated not indicated catalase positive not producted consumed not indicated not producted not indicated not indicated not indicated -Hoeflea marina 10.1099/ijs.0.63291-0 aerobe rod/ bacilli motile non-spore forming Gram-negative not indicated not indicated urease variable catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Hydrotalea flava 10.1099/ijs.0.023002-0 aerobe rod/ bacilli non-motile not indicated Gram-negative not indicated not indicated urease negative catalase positive not indicated not producted not producted not indicated not indicated not indicated not indicated -Streptococcus dysgalactiae 10.1099/00207713-33-2-404 not indicated cocci or oval-shaped not indicated not indicated Gram-positive no growth in 20% bile saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus entericus 10.1099/00207713-52-2-665 facultative anaerobe cocci non-motile not indicated Gram-positive no growth in 20% bile saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus ferus 10.1099/00207713-33-4-883 not indicated cocci not indicated not indicated Gram-positive not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus gallinaceus 10.1099/00207713-52-4-1161 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus gallinarum 10.1099/00207713-32-4-410 not indicated cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus halichoeri 10.1099/ijs.0.63082-0 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus hansenii 10.1099/00207713-24-2-260 obligate anaerobe cocci non-motile not indicated Gram-positive growth in 20% bile saccharolytic not indicated not indicated not indicated major product not producted not indicated not indicated not indicated not indicated -Streptococcus hongkongensis 10.1099/ijs.0.045120-0 facultative anaerobe cocci non-motile non-spore forming Gram-positive growth in 20% bile saccharolytic urease negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus hyointestinalis 10.1099/00207713-38-4-440 facultative anaerobe cocci not indicated not indicated Gram-positive no growth in 20% bile saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus hyovaginalis 10.1099/00207713-47-4-1073 not indicated cocci not indicated not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus ictaluri 10.1099/ijs.0.64810-0 not indicated cocci not indicated not indicated Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus infantarius 10.1099/00207713-50-4-1425 not indicated cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus infantis 10.1099/00207713-48-3-921 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus iniae 10.1099/00207713-26-4-545 facultative anaerobe cocci not indicated not indicated Gram-positive not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus intestinalis 10.1099/00207713-38-3-245 aerotolerant cocci non-motile non-spore forming Gram-positive no growth in 20% bile saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus lactarius 10.1099/ijs.0.021642-0 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus loxodontisalivarius 10.1099/ijs.0.063263-0 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus lutetiensis 10.1099/00207713-52-4-1247 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus macacae 10.1099/00207713-34-3-332 anaerobe (unspecified) cocci not indicated not indicated Gram-positive growth in 20% bile saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus macedonicus 10.1099/00207713-48-2-519 not indicated cocci non-motile not indicated Gram-positive not indicated saccharolytic urease negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus marimammalium 10.1099/ijs.0.63342-0 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic urease variable catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus massiliensis 10.1099/ijs.0.64009-0 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus merionis 10.1099/ijs.0.65823-0 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus minor 10.1099/ijs.0.02818-0 not indicated ovoid not indicated not indicated Gram-positive growth in 20% bile saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus morbillorum 10.1099/00207713-24-2-260 anaerobe (unspecified) cocci non-motile non-spore forming Gram-positive somewhat inhibited by 20% bile saccharolytic urease negative catalase negative major product major product not producted not indicated not indicated not indicated not indicated -Streptococcus moroccensis 10.1099/ijs.0.062893-0 microaerobe or aerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus oligofermentans 10.1099/ijs.0.02493-0 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus oralis 10.1099/00207713-32-4-410 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus oricebi 10.1099/ijsem.0.000834 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus oriloxodontae 10.1099/ijs.0.064048-0 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus orisasini 10.1099/ijs.0.047142-0 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus orisratti 10.1099/00207713-50-1-55 facultative anaerobe cocci non-motile not indicated Gram-positive growth in 20% bile saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus orisuis 10.1099/ijs.0.64741-0 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus ovis 10.1099/00207713-51-3-1147 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus parasuis 10.1099/ijs.0.067116-0 not indicated cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus parvulus 10.1099/00207713-33-1-82 obligate anaerobe cocci non-motile non-spore forming Gram-positive no growth in 20% bile saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Streptococcus pasteurianus 10.1099/00207713-52-4-1247 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus peroris 10.1099/00207713-48-3-921 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus pharyngis 10.1099/ijs.0.000351 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus phocae 10.1099/00207713-44-4-646 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus pleomorphus 10.1099/00221287-102-1-45 obligate anaerobe pleomorphic not indicated not indicated Gram-variable not indicated saccharolytic not indicated catalase negative minor product minor product not indicated minor product not indicated not indicated not indicated -Kocuria rosea 10.1099/00207713-45-4-682 aerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus pluranimalium 10.1099/00207713-49-3-1221 not indicated cocci non-motile not indicated Gram-positive not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus plurextorum 10.1099/ijs.0.65636-0 facultative anaerobe cocci non-motile not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus porci 10.1099/ijs.0.011171-0 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus porcorum 10.1099/ijs.0.022657-0 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus ratti 10.1099/00207713-27-1-26 microaerobe or aerobe cocci not indicated not indicated Gram-positive no growth in 20% bile saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Limnobacter thiooxidans 10.1099/00207713-51-4-1463 not indicated slightly curved rods motile not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Methylobacterium organophilum 10.1099/00207713-26-2-226 aerobe rod/ bacilli motile not indicated Gram-negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Methylophilus methylotrophus 10.1099/00207713-37-4-446 aerobe rods or slightly curved rods motile non-spore forming Gram-negative not indicated saccharolytic urease positive catalase positive consumed consumed not producted not producted not producted not producted not producted -Methyloversatilis universalis 10.1099/ijs.0.64422-0 not indicated not indicated not indicated not indicated not indicated not indicated asaccharolytic urease negative catalase positive consumed not indicated not indicated not indicated not indicated not indicated not indicated -Microlunatus phosphovorus 10.1099/00207713-45-1-17 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase positive not indicated consumed not indicated not indicated not indicated not indicated not indicated -Niastella koreensis 10.1099/ijs.0.64242-0 not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic urease positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Olivibacter sitiensis 10.1099/ijs.0.64561-0 aerobe not indicated not indicated not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Patulibacter minatonensis 10.1099/ijs.0.63796-0 aerobe rod/ bacilli motile non-spore forming Gram-positive not indicated asaccharolytic urease negative catalase positive not indicated consumed consumed not indicated not indicated not indicated not indicated -Wautersiella falsenii 10.1099/ijs.0.64393-0 not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic urease positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Ureaplasma urealyticum 10.1099/00207713-24-2-160 facultative anaerobe cocci or oval-shaped non-motile not indicated Gram-negative not indicated asaccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus rifensis 10.1099/ijs.0.062893-0 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus rubneri 10.1099/ijs.0.048538-0 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Actinobaculum suis 10.1099/00207713-47-3-899 anaerobe (unspecified) pleomorphic non-motile non-spore forming Gram-positive not indicated saccharolytic urease positive catalase negative major product major product not indicated not indicated not indicated not indicated not indicated -Actinomyces europaeus 10.1099/00207713-47-3-687 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Actinomyces neuii 10.1099/00207713-44-1-167 facultative anaerobe rods or oval-shaped non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Alistipes indistinctus 10.1099/ijs.0.014571-0 obligate anaerobe rods or cocci not indicated non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase positive not indicated major product not indicated not indicated not indicated not indicated not indicated -Alistipes inops 10.1099/ijsem.0.000617 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated asaccharolytic urease negative catalase negative not producted not producted not producted not producted not producted not producted not producted -Alistipes onderdonkii 10.1099/ijs.0.64318-0 obligate anaerobe rod/ bacilli not indicated not indicated not indicated growth in 20% bile saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Alistipes shahii 10.1099/ijs.0.64318-0 obligate anaerobe rod/ bacilli not indicated not indicated not indicated growth in 20% bile saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Anaerococcus hydrogenalis 10.1099/00207713-51-4-1521 not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic urease variable not indicated not indicated not indicated not indicated major product not indicated not indicated not indicated -Anaerococcus lactolyticus 10.1099/00207713-51-4-1521 not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic urease positive not indicated not indicated not indicated not indicated major product not indicated not indicated not indicated -Anaerococcus octavius 10.1099/00207713-51-4-1521 not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic urease negative not indicated not indicated not indicated not indicated major product not indicated not indicated not indicated -Anaerococcus vaginalis 10.1099/00207713-51-4-1521 not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic urease negative not indicated not indicated not indicated not indicated major product not indicated not indicated not indicated -Anaerotruncus colihominis 10.1099/ijs.0.02653-0 anaerobe (unspecified) rod/ bacilli not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product not indicated major product not indicated not indicated not indicated -Blautia caecimuris N/A obligate anaerobe cocci or oval-shaped not indicated not indicated Gram-positive not indicated saccharolytic https://www.nature.com/articles/nmicrobiol2016131#Fig3 not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Blautia coccoides 10.1099/ijs.0.65208-0 obligate anaerobe rods or oval-shaped non-motile non-spore forming Gram-positive not indicated saccharolytic 10.1099/00207713-26-4-482 not indicated not indicated not indicated minor product not indicated not indicated not indicated not indicated not indicated -Clostridium purinilyticum 10.1099/00207713-31-2-184 obligate anaerobe rod/ bacilli motile spore forming Gram-positive growth in 20% bile asaccharolytic urease negative catalase negative major product major product not indicated not indicated not indicated not indicated not indicated -Blautia stercoris 10.1099/ijs.0.031625-0 obligate anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Blautia wexlerae 10.1099/ijs.0.65208-0 obligate anaerobe oval-shaped/ coccobaccili not indicated non-spore forming Gram-positive not indicated saccharolytic urease positive catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Bacteroides amylophilus N/A obligate anaerobe pleomorphic rods non-motile not indicated not indicated not indicated saccharolytic http://jb.asm.org/content/72/4/548.full.pdf+html not indicated not indicated major product major product not indicated not indicated not indicated not indicated not indicated -Bacteroides barnesiae 10.1099/ijs.0.64517-0 obligate anaerobe pleomorphic rods non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated minor product -Bacteroides bivius 10.1099/00207713-27-4-337 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic not indicated not indicated not indicated major product not indicated not indicated minor product not indicated major product -Bacteroides buccae 10.1099/00207713-32-1-125 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic not indicated not indicated minor product major product not indicated not indicated minor product not indicated minor product -Bacteroides caccae 10.1099/00207713-36-4-499 not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated major product minor product not indicated minor product not indicated minor product -Bacteroides caecicola 10.1099/ijsem.0.000899 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated major product minor product not indicated not indicated not indicated not indicated -Bacteroides caecigallinarum 10.1099/ijsem.0.000573 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Bacteroides cellulosilyticus 10.1099/ijs.0.64998-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated catalase negative not indicated major product major product not indicated not indicated not indicated not indicated -Bacteroides cellulosolvens 10.1099/00207713-34-2-185 anaerobe (unspecified) rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Bacteroides chinchillae 10.1099/ijs.0.024026-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides clarus 10.1099/ijs.0.015107-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Bacteroides coagulans N/A not indicated oval-shaped/ coccobaccili not indicated not indicated not indicated not indicated not indicated http://jb.asm.org/content/25/4/389.full.pdf+html not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus rupicaprae 10.1099/ijs.0.026187-0 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus saliviloxodontae 10.1099/ijs.0.063263-0 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic urease positive catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus sobrinus 10.1099/00207713-33-4-883 microaerobe cocci not indicated not indicated Gram-positive not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus suis 10.1099/00207713-37-2-160 facultative anaerobe oval-shaped/ coccobaccili non-motile not indicated Gram-positive mixed saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus thoraltensis 10.1099/00207713-47-4-1073 not indicated cocci not indicated not indicated Gram-positive not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus tigurinus 10.1099/ijs.0.038299-0 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus troglodytae 10.1099/ijs.0.039388-0 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic urease positive catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus troglodytidis 10.1099/ijs.0.038133-0 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus urinalis 10.1099/00207713-50-3-1173 facultative anaerobe ovoid non-motile non-spore forming Gram-positive growth in 20% bile saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus ursoris 10.1099/ijs.0.019638-0 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus vestibularis 10.1099/00207713-38-4-335 facultative anaerobe cocci not indicated not indicated Gram-positive somewhat inhibited by 20% bile saccharolytic urease positive catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus waius 10.1099/00207713-49-2-759 facultative anaerobe cocci non-motile non-spore forming Gram-positive no growth in 20% bile saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides coprocola 10.1099/ijs.0.63788-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides coprophilus 10.1099/ijs.0.64979-0 anaerobe (unspecified) rod/ bacilli not indicated non-spore forming Gram-negative growth in 20% bile saccharolytic urease negative not indicated not indicated major product minor product not indicated not indicated not indicated minor product -Bacteroides coprosuis 10.1099/ijs.0.63869-0 anaerobe (unspecified) rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic urease negative catalase negative not indicated major product major product not indicated not indicated not indicated not indicated -Bacteroides corporis 10.1099/00207713-33-1-15 anaerobe (unspecified) cocci not indicated not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated major product not producted not indicated minor product not indicated minor product -Bacteroides disiens 10.1099/00207713-27-4-337 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated minor product major product minor product minor product minor product not indicated minor product -Bacteroides distasonis N/A not indicated rod/ bacilli not indicated not indicated not indicated not indicated saccharolytic http://jb.asm.org/content/25/4/389.full.pdf+html not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides dorei 10.1099/ijs.0.64257-0 anaerobe (unspecified) rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic urease negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides eggerthii 10.1099/00207713-24-2-260 obligate anaerobe pleomorphic rods non-motile not indicated Gram-negative not indicated saccharolytic not indicated not indicated not indicated major product major product not indicated major product not indicated major product -Bacteroides faecichinchillae 10.1099/ijs.0.032706-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides faecis 10.1099/ijs.0.020024-0 anaerobe (unspecified) rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides finegoldii 10.1099/ijs.0.64084-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic urease negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides fluxus 10.1099/ijs.0.015107-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Bacteroides forsythus 10.1099/00207713-36-2-213 obligate anaerobe fusiform not indicated not indicated Gram-negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides gallinaceum 10.1099/ijsem.0.000899 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated minor product -Bacteroides gallinarum 10.1099/ijs.0.64517-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic urease negative catalase negative not indicated minor product major product not indicated not indicated not indicated minor product -Bacteroides gingivalis 10.1099/00207713-30-3-559 obligate anaerobe rods or oval-shaped not indicated not indicated Gram-negative not indicated asaccharolytic not indicated catalase negative not indicated major product major product major product major product not indicated major product -Bacteroides gracilis 10.1099/00207713-31-4-432 microaerobe or anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated asaccharolytic not indicated catalase negative consumed not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides graminisolvens 10.1099/ijs.0.008268-0 not indicated rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic not indicated not indicated not indicated major product major product not indicated not indicated not indicated not indicated -Bacteroides heparinolyticus 10.1099/00207713-35-4-438 obligate anaerobe cocci non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic not indicated catalase negative not indicated minor product minor product not indicated not indicated not indicated minor product -Bacteroides intermedius 10.1099/00207713-33-1-15 anaerobe (unspecified) not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated major product not producted not indicated minor product not indicated minor product -Bacteroides intestinalis 10.1099/ijs.0.63914-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic urease negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides levii 10.1099/00207713-33-1-15 anaerobe (unspecified) not indicated not indicated not indicated not indicated no growth in 20% bile saccharolytic not indicated catalase negative not indicated major product major product major product minor product not indicated major product -Bacteroides loescheii 10.1099/00207713-32-4-399 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated minor product major product not producted not indicated not indicated not indicated not indicated -Bacteroides luti 10.1099/ijs.0.056630-0 not indicated rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Macteroides macacae 10.1099/00207713-30-3-559 obligate anaerobe rods or cocci not indicated not indicated Gram-negative not indicated not indicated not indicated catalase positive not indicated major product major product minor product minor product not indicated minor product -Bacteroides massiliensis 10.1099/ijs.0.63350-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides microfusus 10.1099/00207713-28-4-478 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic urease negative catalase negative not indicated major product major product not producted not producted not indicated not producted -Bacteroides multiacidus 10.1099/00207713-24-1-35 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Bacteroides oleiciplenus 10.1099/ijs.0.015107-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated major product major product not indicated not indicated not indicated not indicated not indicated -Bacteroides oralis N/A obligate anaerobe not indicated non-motile not indicated Gram-negative no growth in 20% bile saccharolytic http://jb.asm.org/content/88/5/1329.full.pdf+html not indicated catalase negative major product major product not indicated not indicated not indicated not indicated not indicated -Bacteroides oris 10.1099/00207713-32-1-125 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic not indicated not indicated not indicated major product not indicated not indicated minor product not indicated minor product -Bacteroides oulorum 10.1099/00207713-35-2-193 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Bacteroides paurosaccharolyticus 10.1099/ijs.0.022566-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated major product major product not indicated not indicated not indicated not indicated -Bacteroides plebeius 10.1099/ijs.0.63788-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides propionicifaciens 10.1099/ijs.0.65486-0 not indicated rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase variable not indicated major product major product not indicated not indicated not indicated not indicated -Bacteroides reticulotermitis 10.1099/ijs.0.040931-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated major product minor product not indicated not indicated not indicated not indicated -Bacteroides ruminicola N/A obligate anaerobe rods or oval-shaped non-motile not indicated Gram-negative not indicated saccharolytic http://jb.asm.org/content/76/1/15.full.pdf+html not indicated not indicated major product major product not indicated not indicated not indicated not indicated not indicated -Bacteroides salanitronis 10.1099/ijs.0.64517-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated minor product -Bacteroides salivosus 10.1099/00207713-37-4-307 obligate anaerobe rods or cocci non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated catalase positive not indicated major product not producted major product minor product not indicated minor product -Bacteroides stercorirosoris 10.1099/ijs.0.032706-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides stercoris 10.1099/00207713-36-4-499 not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic not indicated not indicated major product major product major product not indicated minor product not indicated minor product -Bacteroides tectus 10.1099/00207713-36-2-123 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative growth in 20% bile mixed not indicated catalase negative not indicated major product major product not indicated minor product not indicated minor product -Bacteroides uniformis N/A not indicated rod/ bacilli not indicated not indicated not indicated not indicated saccharolytic http://jb.asm.org/content/25/4/389.full.pdf+html not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides ureolyticus 10.1099/00207713-28-2-197 anaerobe (unspecified) rod/ bacilli variable not indicated Gram-negative not indicated asaccharolytic urease positive catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides veroralis 10.1099/00207713-33-1-57 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bacteroides zoogleoformans 10.1099/00207713-32-3-271 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated major product minor product not indicated not indicated not indicated minor product -Prevotella aurantiaca 10.1099/ijs.0.012831-0 obligate anaerobe rods or oval-shaped non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Prevotella baroniae 10.1099/ijs.0.63634-0 obligate anaerobe rods or cocci non-motile not indicated Gram-negative no growth in 20% bile saccharolytic not indicated catalase negative not indicated major product not indicated not indicated minor product not indicated minor product -Prevotella bergensis 10.1099/ijs.0.63888-0 obligate anaerobe slightly curved rods non-motile not indicated Gram-negative no growth in 20% bile saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated minor product -Prevotella colorans 10.1099/ijsem.0.001134 obligate anaerobe pleomorphic rods non-motile not indicated Gram-negative not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Prevotella copri 10.1099/ijs.0.64778-0 anaerobe (unspecified) rod/ bacilli not indicated non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Prevotella dentalis 10.1099/00207713-45-4-832 obligate anaerobe oval-shaped/ coccobaccili non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Prevotella dentasini 10.1099/ijs.0.017020-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Prevotella enoeca 10.1099/00207713-44-4-599 not indicated not indicated non-motile not indicated not indicated not indicated not indicated not indicated not indicated minor product major product not indicated not indicated not indicated not indicated not indicated -Prevotella falsenii 10.1099/ijs.0.002626-0 obligate anaerobe rods or oval-shaped non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Prevotella fusca 10.1099/ijs.0.023861-0 obligate anaerobe rod/ bacilli non-motile not indicated Gram-negative no growth in 20% bile saccharolytic not indicated catalase negative not indicated major product not indicated not indicated minor product not indicated minor product -Prevotella histicola 10.1099/ijs.0.65656-0 obligate anaerobe rod/ bacilli non-motile not indicated Gram-negative no growth in 20% bile saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated minor product -Prevotella jejuni 10.1099/ijs.0.052647-0 obligate anaerobe rod/ bacilli non-motile not indicated Gram-negative not indicated saccharolytic not indicated not indicated not indicated major product not indicated not indicated not indicated not indicated minor product -Prevotella maculosa 10.1099/ijs.0.65281-0 obligate anaerobe rod/ bacilli non-motile not indicated Gram-negative no growth in 20% bile saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Prevotella marshii 10.1099/ijs.0.63634-0 obligate anaerobe rod/ bacilli non-motile not indicated Gram-negative no growth in 20% bile saccharolytic not indicated catalase negative not indicated major product major product not indicated not indicated not indicated not indicated -Prevotella micans 10.1099/ijs.0.002337-0 obligate anaerobe rod/ bacilli non-motile not indicated Gram-negative no growth in 20% bile saccharolytic not indicated catalase negative not indicated major product not indicated not indicated minor product not indicated major product -Prevotella multiformis 10.1099/ijs.0.63451-0 obligate anaerobe rods or cocci non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated minor product -Prevotella multisaccharivorax 10.1099/ijs.0.63739-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated minor product -Prevotella nanceiensis 10.1099/ijs.0.65173-0 obligate anaerobe rods or cocci non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Prevotella nigrescens 10.1099/00207713-42-4-542 obligate anaerobe rod/ bacilli not indicated non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated major product not indicated not indicated major product not indicated major product -Prevotella oryzae 10.1099/ijs.0.038638-0 not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Prevotella pallens 10.1099/00207713-48-1-47 obligate anaerobe rods or oval-shaped non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated major product not indicated not indicated not indicated not indicated major product -Prevotella paludivivens 10.1099/ijs.0.64914-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Prevotella pleuritidis 10.1099/ijs.0.64885-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Prevotella saccharolytica 10.1099/ijs.0.014720-0 obligate anaerobe rod/ bacilli non-motile not indicated Gram-negative no growth in 20% bile saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Prevotella salivae 10.1099/ijs.0.02876-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated minor product -Prevotella scopos 10.1099/ijs.0.023861-0 obligate anaerobe rod/ bacilli non-motile not indicated Gram-negative no growth in 20% bile saccharolytic not indicated catalase negative not indicated major product not indicated not indicated minor product not indicated major product -Prevotella shahii 10.1099/ijs.0.02876-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Barnesiella intestinihominis 10.1099/ijs.0.2008/000810-0 obligate anaerobe pleomorphic non-motile non-spore forming Gram-negative not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter hominis 10.1099/00207713-51-2-651 anaerobe (unspecified) rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter ureolyticus 10.1099/ijs.0.017152-0 anaerobe (unspecified) rod/ bacilli non-motile not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Clostridium bartlettii 10.1016/j.anaerobe.2004.04.004 obligate anaerobe rod/ bacilli variable mixed Gram-positive somewhat inhibited by 20% bile saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Corynebacterium aurimucosum 10.1099/00207713-52-3-1001 facultative anaerobe pleomorphic non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Corynebacterium tuberculostearicum 10.1099/ijs.0.02907-0 facultative anaerobe pleomorphic rods non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Dialister invisus 10.1099/ijs.0.02640-0 obligate anaerobe cocci non-motile not indicated Gram-negative no growth in 20% bile asaccharolytic not indicated not indicated not indicated minor product not indicated not indicated not indicated not indicated not indicated -Dialister micraerophilus 10.1099/ijs.0.63715-0 microaerobe or anaerobe cocci non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Prevotella stercorea 10.1099/ijs.0.64778-0 anaerobe (unspecified) rod/ bacilli not indicated non-spore forming Gram-negative no growth in 20% bile saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated minor product -Prevotella tannerae 10.1099/00207713-44-4-599 not indicated not indicated non-motile not indicated not indicated not indicated saccharolytic not indicated not indicated minor product major product not indicated not indicated minor product not indicated minor product -Prevotella timonensis 10.1099/ijs.0.64609-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Ruminococcus gauvreauii 10.1099/ijs.0.65259-0 obligate anaerobe cocci non-motile not indicated Gram-positive not indicated saccharolytic urease negative catalase negative not producted major product not producted not producted not producted not producted not producted -Ruminococcus torques 10.1099/00207713-24-2-260 obligate anaerobe cocci or oval-shaped non-motile not indicated Gram-positive growth in 20% bile saccharolytic not indicated not indicated major product major product not producted not indicated not indicated not indicated not indicated -Eubacterium brachy 10.1099/00207713-30-1-163 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated minor product minor product not indicated not indicated major product not indicated major product -Eubacterium callanderi 10.1099/00207713-38-3-254 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated major product consumed not indicated major product not indicated not indicated not indicated -Eubacterium cellulosolvens N/A obligate anaerobe cocci motile not indicated Gram-variable not indicated saccharolytic http://jb.asm.org/content/76/5/529.full.pdf+html not indicated catalase negative major product major product not producted not producted not indicated not indicated not indicated -Veillonella atypica 10.1099/00207713-32-1-28 anaerobe (unspecified) cocci non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated major product major product not indicated not indicated not indicated not indicated -Propionimicrobium lymphophilum 10.1099/00207713-52-6-1925 anaerobe (unspecified) cocci non-motile non-spore forming Gram-positive somewhat inhibited by 20% bile saccharolytic not indicated catalase positive minor product major product major product not indicated not indicated not indicated major product -Porphyromonas bennonis 10.1099/ijs.0.001909-0 obligate anaerobe rod/ bacilli not indicated non-spore forming Gram-negative not indicated asaccharolytic urease negative catalase variable not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Peptostreptococcus stomatis 10.1099/ijs.0.64041-0 obligate anaerobe cocci not indicated not indicated Gram-positive not indicated saccharolytic urease negative catalase negative not indicated major product not indicated minor product minor product not indicated minor product -Peptoniphilus lacrimalis 10.1099/00207713-51-4-1521 obligate anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Peptoniphilus duerdenii 10.1099/ijs.0.031997-0 obligate anaerobe cocci not indicated not indicated Gram-positive somewhat inhibited by 20% bile asaccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Eubacterium coprostanoligenes 10.1099/00207713-44-1-137 aerotolerant oval-shaped/ coccobaccili non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated major product major product not indicated not indicated not indicated not indicated not indicated -Eubacterium dolichum 10.1099/00207713-26-2-238 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated minor product not indicated major product not indicated not indicated not indicated -Eubacterium exiguum 10.1099/00207713-46-4-1120 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-variable not indicated asaccharolytic urease negative catalase negative not producted not producted not producted not producted not producted not producted not producted -Eubacterium formicigenerans 0.1099/00207713-24-2-260 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative not indicated major product major product not producted not indicated not indicated not indicated not indicated -Eubacterium fossor 10.1099/00207713-36-3-383 obligate anaerobe rods or oval-shaped non-motile not indicated Gram-positive growth in 20% bile saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Eubacterium hadrum 10.1099/00207713-26-2-238 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative not indicated minor product major product minor product major product not indicated not indicated not indicated -Eubacterium infirmum 10.1099/00207713-46-4-957 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated urease negative catalase negative not indicated major product not indicated major product not indicated not indicated not indicated -Eubacterium minutum 10.1099/00207713-46-1-31 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-variable not indicated asaccharolytic urease negative catalase negative not producted not producted not producted major product not producted not producted not producted -Eubacterium nodatum 10.1099/00207713-30-1-163 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated not indicated not indicated minor product minor product not indicated major product not indicated not indicated not indicated -Eubacterium plautii 10.1099/00207713-32-3-346 not indicated rods or slightly curved rods non-motile not indicated Gram-variable not indicated not indicated not indicated not indicated not indicated minor product not indicated major product not indicated not indicated not indicated -Eubacterium plexicaudatum 10.1099/00207713-24-4-408 anaerobe (unspecified) rods or slightly curved rods motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated major product not indicated major product not indicated not indicated not indicated -Eubacterium pyruvativorans 10.1099/ijs.0.02110-0 obligate anaerobe rods or slightly curved rods non-motile mixed Gram-positive not indicated asaccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Eubacterium ramulus 10.1099/00207713-26-2-238 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative not indicated major product major product not indicated major product not indicated not indicated not indicated -Eubacterium ruminantium N/A obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic http://mmbr.asm.org/content/23/3/125.full.pdf+html not indicated not indicated major product major product not indicated major product not indicated not indicated not indicated -Eubacterium saphenum 10.1099/00207713-43-2-302 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-variable not indicated asaccharolytic urease negative catalase negative not indicated major product not indicated major product not indicated not indicated not indicated -Eubacterium suis 10.1099/00207713-32-2-218 anaerobe (unspecified) pleomorphic rods non-motile non-spore forming Gram-positive not indicated saccharolytic urease positive catalase negative major product major product not indicated not indicated not indicated not indicated not indicated -Eubacterium tardum 10.1099/00207713-46-4-957 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated urease negative catalase negative not indicated not indicated not indicated major product not indicated not indicated not indicated -Eubacterium timidum 10.1099/00207713-30-1-163 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated not indicated not indicated minor product minor product not indicated not indicated not indicated not indicated not indicated -Eubacterium uniforme 10.1099/00207713-35-3-323 obligate anaerobe rods or cocci non-motile not indicated Gram-variable not indicated not indicated not indicated catalase negative major product major product consumed not indicated not indicated not indicated not indicated -Eubacterium xylanophilum 10.1099/00207713-35-3-323 obligate anaerobe rods or cocci motile non-spore forming not indicated not indicated saccharolytic not indicated catalase negative major product major product not indicated major product not indicated not indicated not indicated -Eubacterium yurii 10.1099/00207713-36-2-145 obligate anaerobe rod/ bacilli motile non-spore forming Gram-positive not indicated mixed not indicated catalase negative not indicated minor product minor product major product not indicated not indicated not indicated -Helicobacter acinonychis 10.1099/00207713-43-1-99 microaerobe rod/ bacilli motile non-spore forming Gram-negative not indicated not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helicobacter apri 10.1099/ijsem.0.001071 microaerobe spirals not indicated non-spore forming Gram-negative no growth in 20% bile not indicated urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helicobacter baculiformis 10.1099/ijs.0.65152-0 microaerobe rods or cocci motile non-spore forming Gram-negative no growth in 20% bile not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helicobacter bizzozeronii 10.1099/00207713-46-1-160 not indicated spirals or cocci motile non-spore forming Gram-negative no growth in 20% bile not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helicobacter cynogastricus 10.1099/ijs.0.63860-0 microaerobe or anaerobe spirals or cocci motile non-spore forming Gram-negative no growth in 20% bile not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helicobacter equorum 10.1099/ijs.0.64279-0 microaerobe rods or cocci motile non-spore forming Gram-negative no growth in 20% bile saccharolytic urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helicobacter felis 10.1099/00207713-41-1-31 microaerobe or anaerobe spirals or cocci motile non-spore forming Gram-negative not indicated asaccharolytic urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helicobacter ganmani 10.1099/00207713-51-5-1881 obligate anaerobe spiral or curved rods not indicated not indicated not indicated growth in 2% bile not indicated urease negative catalase variable not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helicobacter heilmannii 10.1099/ijs.0.029207-0 microaerobe or anaerobe spirals or cocci motile non-spore forming Gram-negative no growth in 20% bile not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helicobacter himalayensis 10.1099/ijs.0.000163 microaerobe or anaerobe slightly curved rods motile non-spore forming Gram-negative no growth in 20% bile not indicated urease negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helicobacter muridarum 10.1099/00207713-42-1-27 microaerobe spirals motile non-spore forming Gram-negative no growth in 20% bile not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helicobacter nemestrinae 10.1099/00207713-41-1-148 microaerobe or anaerobe pleomorphic motile not indicated Gram-negative no growth in 20% bile asaccharolytic urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helicobacter pametensis 10.1099/00207713-44-3-553 microaerobe or anaerobe slightly curved rods motile non-spore forming Gram-negative not indicated not indicated not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helicobacter rodentium 10.1099/00207713-47-3-627 microaerobe or anaerobe spiral or curved rods motile non-spore forming Gram-negative not indicated not indicated urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helicobacter salomonis 10.1099/00207713-47-4-975 not indicated spirals or cocci motile non-spore forming Gram-negative no growth in 20% bile not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helicobacter suis 10.1099/ijs.0.65133-0 microaerobe or anaerobe spirals or cocci motile not indicated not indicated no growth in 20% bile not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helicobacter valdiviensis 10.1099/ijs.0.057141-0 microaerobe rods or cocci motile non-spore forming Gram-negative not indicated saccharolytic urease variable catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Gemella asaccharolytica 10.1099/ijs.0.001966-0 obligate anaerobe cocci non-motile not indicated Gram-variable not indicated asaccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Gemella cuniculi 10.1099/00207713-50-6-2037 facultative anaerobe cocci non-motile not indicated Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Gemella morbillorum 10.1099/00207713-38-4-442 aerotolerant cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated minor product minor product not producted not indicated not indicated not indicated not indicated -Gemella palaticanis 10.1099/00207713-49-4-1523 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Gemella parahaemolysans 10.1099/ijs.0.052795-0 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Gemella taiwanensis 10.1099/ijs.0.052795-0 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Rothia aerobat 10.1099/ijsem.0.001153 aerobe rods or cocci non-motile non-spore forming Gram-positive not indicated saccharolytic urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter avium 10.1099/ijs.0.007419-0 microaerobe spirals motile not indicated Gram-negative mixed not indicated urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Rothia amarae 10.1099/00207713-52-6-2257 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated mixed urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter canadensis 10.1099/ijs.0.65061-0 microaerobe or anaerobe cocci or curved rods motile not indicated Gram-negative not indicated not indicated urease variable catalase variable not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter coli 10.1099/00207713-23-2-122 aerotolerant not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter corcagiensis 10.1099/ijs.0.063867-0 microaerobe or anaerobe rod/ bacilli motile not indicated Gram-negative growth in 2% bile not indicated urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter cryaerophilus 10.1099/00207713-35-3-342 facultative anaerobe spiral or curved rods not indicated non-spore forming Gram-negative not indicated asaccharolytic urease negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter cuniculorum 10.1099/ijs.0.007286-0 microaerobe spirals motile not indicated Gram-negative mixed not indicated urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter hyoilei 10.1099/00207713-45-1-61 microaerobe or anaerobe slightly curved rods motile non-spore forming Gram-negative not indicated not indicated urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter iguaniorum 10.1099/ijs.0.000048 microaerobe or anaerobe spiral or curved rods not indicated not indicated Gram-negative not indicated not indicated not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Rothia endophytica 10.1099/ijs.0.052522-0 anaerobe (unspecified) ovoid non-motile non-spore forming Gram-positive not indicated saccharolytic urease positive catalase positive not indicated not producted not producted not indicated not indicated not indicated not indicated -Rothia terrae 10.1099/ijs.0.65172-0 facultative anaerobe ovoid non-motile non-spore forming Gram-positive not indicated saccharolytic urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Pseudobutyrivibrio xylanivorans 10.1099/ijs.0.02345-0 anaerobe (unspecified) rods or slightly curved rods motile non-spore forming Gram-negative not indicated saccharolytic urease negative catalase negative minor product consumed not indicated minor product not indicated not indicated not indicated -Peptococcus simiae 10.1099/ijsem.0.001494 obligate anaerobe cocci non-motile non-spore forming Gram-positive growth in 20% bile not indicated urease negative catalase variable not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Paraprevotella xylaniphila 10.1099/ijs.0.008169-0 obligate anaerobe not indicated non-motile non-spore forming Gram-negative not indicated saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Anaerostipes butyraticus 10.1099/ijs.0.015289-0 anaerobe (unspecified) rod/ bacilli non-motile spore forming Gram-positive not indicated saccharolytic urease negative not indicated not indicated consumed consumed major product not indicated not indicated not indicated -Anaerostipes rhamnosivorans 10.1099/ijs.0.055061-0 anaerobe (unspecified) rod/ bacilli non-motile spore forming Gram-variable not indicated not indicated urease negative catalase negative major product major product not indicated major product not indicated not indicated not indicated -Butyrivibrio hungatei 10.1099/ijs.0.02345-0 anaerobe (unspecified) rods or slightly curved rods motile non-spore forming Gram-negative not indicated saccharolytic urease negative catalase negative major product major product not indicated major product not indicated not indicated not indicated -Butyrivibrio proteoclasticus 10.1099/ijs.0.65845-0 obligate anaerobe rods or slightly curved rods motile non-spore forming Gram-positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated major product not indicated not indicated not indicated -Granulicella paludicola 10.1099/ijs.0.021824-0 aerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated mixed urease negative catalase positive not producted not producted not indicated not producted not indicated not producted not indicated -Mobiluncus curtisii 10.1099/00207713-34-2-177 anaerobe (unspecified) slightly curved rods motile non-spore forming Gram-variable not indicated saccharolytic not indicated not indicated not indicated major product not indicated not producted not indicated not indicated not indicated -Megamonas funiformis 10.1099/ijs.0.65456-0 anaerobe (unspecified) rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Odoribacter laneus 10.1099/ijs.0.014571-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated asaccharolytic urease negative catalase negative not indicated minor product not indicated not indicated not indicated not indicated minor product -Mogibacterium diversum 10.1099/00207713-52-1-115 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Mogibacterium neglectum 10.1099/00207713-52-1-115 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter insulaenigrae 10.1099/ijs.0.63147-0 microaerobe slightly curved rods motile non-spore forming Gram-negative not indicated not indicated urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Fusibacter bizertensis 10.1099/ijs.0.066183-0 not indicated rod/ bacilli motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated consumed major product consumed consumed not indicated not indicated not indicated -Fusibacter fontis 10.1099/ijsem.0.000445 not indicated rod/ bacilli motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated consumed major product consumed consumed not indicated not indicated not indicated -Campylobacter jejuni 10.1099/00207713-23-2-122 microaerobe slightly curved rods motile not indicated not indicated not indicated not indicated not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Fusibacter paucivorans 10.1099/00207713-49-3-1141 obligate anaerobe fusiform motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated major product not indicated major product not indicated not indicated not indicated -Campylobacter lanienae 10.1099/00207713-50-2-865 microaerobe or anaerobe rod/ bacilli motile non-spore forming Gram-negative not indicated asaccharolytic urease negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Fusibacter tunisiensis 10.1099/ijs.0.034603-0 anaerobe (unspecified) rod/ bacilli motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated major product not indicated major product not indicated not indicated not indicated -Campylobacter mucosalis 10.1099/00207713-35-2-189 microaerobe spirals, cocci, or curved rods motile not indicated Gram-negative not indicated not indicated not indicated not indicated consumed not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter mustelae 10.1099/00207713-39-3-301 anaerobe (unspecified) not indicated motile not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter nitrofigilis 10.1099/00207713-33-3-605 anaerobe (unspecified) cocci or curved rods motile not indicated Gram-negative mixed asaccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter peloridis 10.1099/ijs.0.000851-0 not indicated slightly curved rods not indicated not indicated Gram-negative not indicated not indicated not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter showae 10.1099/00207713-43-4-631 microaerobe rod/ bacilli motile not indicated Gram-negative not indicated asaccharolytic urease negative not indicated consumed not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter sputorum 10.1099/00207713-23-2-122 microaerobe not indicated not indicated not indicated not indicated not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter subantarcticus 10.1099/ijs.0.011056-0 microaerobe or anaerobe slightly curved rods motile not indicated Gram-negative growth in 2% bile not indicated not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Campylobacter volucris 10.1099/ijs.0.013748-0 microaerobe or anaerobe not indicated motile non-spore forming Gram-negative growth in 2% bile not indicated not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Coprococcus comes 10.1099/00207713-24-2-260 obligate anaerobe cocci non-motile not indicated Gram-positive somewhat inhibited by 20% bile saccharolytic not indicated not indicated minor product major product not producted major product not indicated not indicated not indicated -Alkaliphilus crotonatoxidans 10.1099/ijs.0.02373-0 obligate anaerobe rods or slightly curved rods motile spore forming Gram-positive not indicated mixed not indicated not indicated not indicated not producted not indicated not producted not indicated not indicated not indicated -Alkaliphilus halophilus 10.1099/ijs.0.014084-0 obligate anaerobe rods or slightly curved rods motile spore forming Gram-positive not indicated saccharolytic not indicated not indicated major product major product not indicated not indicated not indicated not indicated not indicated -Alkaliphilus transvaalensis 10.1099/00207713-51-4-1245 obligate anaerobe rods or slightly curved rods motile spore forming Gram-positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Acetivibrio cellulolyticus 10.1099/00207713-36-2-314 anaerobe (unspecified) rods or slightly curved rods motile not indicated Gram-negative not indicated not indicated urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Desulfitobacterium aromaticivorans 10.1099/ijs.0.003525-0 obligate anaerobe slightly curved rods motile spore forming Gram-positive not indicated not indicated not indicated not indicated not indicated consumed not indicated not indicated not indicated not indicated not indicated -Desulfitobacterium hafniense 10.1099/00207713-46-2-442 obligate anaerobe rod/ bacilli motile spore forming Gram-negative not indicated asaccharolytic not indicated catalase negative not consumed major product not consumed not consumed not indicated not indicated not indicated -Desulfitobacterium metallireducens 10.1099/00207713-52-6-1929 obligate anaerobe slightly curved rods non-motile not indicated Gram-positive not indicated not indicated not indicated not indicated consumed not consumed not indicated consumed not consumed not indicated not indicated -Caloramator australicus 10.1099/ijs.0.000802-0 obligate anaerobe slightly curved rods motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated not consumed not consumed not consumed not indicated not indicated not indicated not indicated -Caloramator boliviensis 10.1099/ijs.0.032664-0 obligate anaerobe rods or slightly curved rods motile spore forming Gram-variable not indicated saccharolytic not indicated not indicated not indicated minor product minor product not indicated not indicated not indicated not indicated -Caloramator coolhaasii 10.1099/00207713-50-3-1155 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated major product minor product not indicated not indicated not indicated not indicated -Caloramator indicus 10.1099/00207713-46-2-497 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Caloramator mitchellensis 10.1099/ijs.0.023655-0 obligate anaerobe slightly curved rods motile non-spore forming Gram-variable not indicated saccharolytic not indicated not indicated not indicated major product not consumed not indicated not indicated not indicated not indicated -Caloramator proteoclasticus 10.1099/00207713-47-3-651 obligate anaerobe rods or slightly curved rods motile spore forming Gram-negative not indicated saccharolytic not indicated not indicated major product major product major product major product not indicated not indicated not indicated -Caloramator quimbayensis 10.1099/ijs.0.037937-0 obligate anaerobe rods or slightly curved rods motile spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated major product not consumed not consumed not indicated not indicated not indicated -Caloramator viterbiensis 10.1099/00207713-52-4-1177 not indicated rods or slightly curved rods non-motile spore forming Gram-positive not indicated saccharolytic not indicated not indicated not consumed not consumed not consumed not indicated not indicated not indicated not indicated -Veillonella caviae 10.1099/00207713-32-1-28 obligate anaerobe not indicated non-motile non-spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated major product major product not indicated not indicated not indicated not indicated -Facklamia miroungae 10.1099/00207713-51-4-1401 facultative anaerobe ovoid non-motile non-spore forming Gram-positive not indicated mixed urease positive catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Facklamia sourekii 10.1099/00207713-49-2-635 facultative anaerobe ovoid non-motile non-spore forming Gram-positive not indicated mixed urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Facklamia tabacinasalis 10.1099/00207713-49-3-1247 facultative anaerobe cocci not indicated non-spore forming Gram-positive not indicated not indicated urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Acetivibrio cellulosolvens 10.1099/00207713-34-4-419 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated not indicated urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Acetivibrio ethanolgignens 10.1099/00207713-31-3-333 obligate anaerobe slightly curved rods motile non-spore forming Gram-negative no growth in 20% bile not indicated urease negative catalase negative not indicated major product not producted not indicated not indicated not indicated not indicated -Veillonella tobetsuensis 10.1099/ijs.0.042515-0 obligate anaerobe cocci non-motile non-spore forming Gram-negative not indicated not indicated urease negative catalase negative not indicated major product major product not indicated not indicated not indicated not indicated -Veillonella seminalis 10.1099/ijs.0.064451-0 anaerobe (unspecified) cocci non-motile non-spore forming Gram-negative not indicated not indicated urease negative catalase negative not indicated major product major product not indicated not indicated not indicated not indicated -Veillonella rogosae 10.1099/ijs.0.65093-0 obligate anaerobe cocci non-motile non-spore forming Gram-negative not indicated not indicated not indicated catalase negative not indicated major product major product not indicated not indicated not indicated not indicated -Veillonella rodentium 10.1099/00207713-32-1-28 anaerobe (unspecified) cocci non-motile non-spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated major product major product not indicated not indicated not indicated not indicated -Veillonella ratti 10.1099/00207713-32-1-28 anaerobe (unspecified) cocci non-motile non-spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated major product major product not indicated not indicated not indicated not indicated -Veillonella montpellierensis 10.1099/ijs.0.02952-0 obligate anaerobe cocci non-motile non-spore forming Gram-negative not indicated not indicated urease negative catalase variable not indicated major product major product not indicated not indicated not indicated not indicated -Veillonella magna 10.1099/ijs.0.2008/001032-0 anaerobe (unspecified) cocci non-motile non-spore forming Gram-negative not indicated not indicated not indicated catalase negative not indicated minor product major product not indicated not indicated not indicated not indicated -Veillonella dispar 10.1099/00207713-32-1-28 anaerobe (unspecified) cocci non-motile non-spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated major product major product not indicated not indicated not indicated not indicated -Veillonella denticariosi 10.1099/ijs.0.65096-0 obligate anaerobe cocci non-motile non-spore forming Gram-negative not indicated not indicated not indicated catalase negative not indicated major product major product not indicated not indicated not indicated not indicated -Veillonella criceti 10.1099/00207713-32-1-28 anaerobe (unspecified) cocci non-motile non-spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated major product major product not indicated not indicated not indicated not indicated -Caminicella sporogenes 10.1099/00207713-52-5-1621 anaerobe (unspecified) rod/ bacilli motile spore forming Gram-negative not indicated saccharolytic not indicated not indicated major product major product not indicated major product not indicated not indicated not indicated -Cellulosibacter alkalithermophilus 10.1099/ijs.0.027854-0 obligate anaerobe rods or slightly curved rods motile spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product major product major product not indicated not indicated not indicated -Caloranaerobacter azorensis 10.1099/00207713-51-5-1789 anaerobe (unspecified) rod/ bacilli motile non-spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Caloranaerobacter ferrireducens 10.1099/ijs.0.000165 obligate anaerobe rod/ bacilli motile non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Garciella nitratireducens 10.1099/ijs.0.02662-0 obligate anaerobe rod/ bacilli motile spore forming Gram-positive not indicated saccharolytic not indicated not indicated not consumed not consumed not consumed not consumed not indicated not indicated not indicated -Guggenheimella bovis 10.1099/ijs.0.63116-0 obligate anaerobe rods or cocci non-motile non-spore forming Gram-positive not indicated asaccharolytic not indicated not indicated not indicated minor product minor product major product minor product not indicated minor product -Hespellia porcina 10.1099/ijs.0.02719-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative major product major product major product not indicated not indicated not indicated not indicated -Hespellia stercorisuis 10.1099/ijs.0.02719-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative major product major product major product not indicated not indicated not consumed not indicated -Soehngenia saccharolytica 10.1099/ijs.0.02668-0 anaerobe (unspecified) rod/ bacilli motile spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Alistipes putredinis 10.1002/9781118960608.gbm00251 not indicated rods or slightly curved rods not indicated not indicated not indicated no growth in 20% bile asaccharolytic not indicated catalase positive not indicated minor product minor product not indicated not indicated not indicated minor product -Alistipes finegoldii 10.1002/9781118960608.gbm00251 not indicated rod/ bacilli not indicated not indicated not indicated growth in 20% bile saccharolytic not indicated catalase negative not indicated minor product minor product not indicated not indicated not indicated minor product -Bacteroides fragilis 10.1002/9781118960608.gbm00238 anaerobe (unspecified) rod/ bacilli non-motile not indicated Gram-negative growth in 20% bile saccharolytic not indicated catalase positive not indicated major product minor product not indicated minor product not indicated minor product -Bifidobacterium bifidum 10.1002/9781118960608.gbm00019 microaerobe not indicated non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Clostridium asparagiforme 10.1002/9781118960608.gbm00619 anaerobe (unspecified) rod/ bacilli not indicated spore forming Gram-positive not indicated saccharolytic not indicated not indicated minor product major product not indicated not indicated not indicated not indicated not indicated -Clostridium bifermentans 10.1002/9781118960608.gbm00619 not indicated rod/ bacilli motile spore forming Gram-positive no growth in 20% bile saccharolytic not indicated not indicated major product major product minor product minor product minor product not indicated minor product -Clostridium bolteae 10.1002/9781118960608.gbm00619 obligate anaerobe rod/ bacilli not indicated mixed Gram-positive not indicated saccharolytic not indicated not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Clostridium citroniae 10.1002/9781118960608.gbm00619 not indicated rod/ bacilli not indicated mixed Gram-negative not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Tepidibacter formicigenes 10.1099/ijs.0.02836-0 anaerobe (unspecified) rod/ bacilli motile spore forming Gram-positive not indicated not indicated not indicated not indicated major product minor product not indicated not indicated not indicated not indicated not indicated -Tepidibacter mesophilus 10.1099/ijs.0.027409-0 anaerobe (unspecified) rod/ bacilli motile spore forming Gram-positive not indicated saccharolytic urease positive catalase negative consumed consumed not indicated consumed not indicated not indicated not indicated -Tepidibacter thalassicus 10.1099/ijs.0.02600-0 anaerobe (unspecified) rods or slightly curved rods motile spore forming Gram-positive not indicated mixed not indicated not indicated not consumed major product not indicated not consumed not indicated not indicated not indicated -Clostridium clostridioforme 10.1002/9781118960608.gbm00619 not indicated rod/ bacilli variable spore forming not indicated mixed not indicated not indicated not indicated major product major product minor product not indicated not indicated not indicated not indicated -Clostridium cochlearium 10.1002/9781118960608.gbm00619 not indicated rods or slightly curved rods motile spore forming not indicated no growth in 20% bile not indicated not indicated not indicated minor product major product major product major product not indicated not indicated not indicated -Tepidimicrobium ferriphilum 10.1099/ijs.0.63694-0 anaerobe (unspecified) rods or slightly curved rods motile non-spore forming Gram-positive not indicated asaccharolytic not indicated not indicated not consumed not consumed not consumed not consumed not indicated not indicated not indicated -Tepidimicrobium xylanilyticum 10.1099/ijs.0.005124-0 anaerobe (unspecified) rods or slightly curved rods motile mixed Gram-positive not indicated not indicated not indicated not indicated not indicated major product minor product major product not indicated not indicated not indicated -Desulfotomaculum alcoholivorax 10.1099/ijs.0.65025-0 not indicated rod/ bacilli motile spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Thermicola carboxydiphila 10.1099/ijs.0.63299-0 obligate anaerobe rod/ bacilli motile non-spore forming Gram-positive not indicated not indicated not indicated not indicated not consumed not consumed not indicated not indicated not indicated not indicated not indicated -Thermohalobacter berrensis 10.1099/00207713-50-2-559 obligate anaerobe rod/ bacilli motile non-spore forming Gram-negative not indicated not indicated not indicated not indicated not consumed major product not indicated not indicated not indicated not indicated not indicated -Desulfotomaculum alkaliphilum 10.1099/00207713-50-1-25 obligate anaerobe curved rods non-motile spore forming Gram-positive not indicated not indicated not indicated not indicated consumed not indicated not indicated not indicated not indicated not indicated not indicated -Thermoterrabacterium ferrireducens 10.1099/00207713-47-2-541 anaerobe (unspecified) rods or slightly curved rods motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated not consumed major product not consumed not indicated not indicated not indicated not indicated -Carboxydothermus ferrireducens 10.1099/ijs.0.64503-0 anaerobe (unspecified) rods or slightly curved rods motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated major product not consumed not indicated not indicated not indicated not indicated -Carboxydothermus islandicus 10.1099/ijs.0.030288-0 obligate anaerobe rods or slightly curved rods motile non-spore forming Gram-positive not indicated not indicated not indicated not indicated not consumed not consumed not indicated not indicated not indicated not indicated not indicated -Carboxydothermus pertinax 10.1099/ijs.0.031583-0 anaerobe (unspecified) rod/ bacilli motile non-spore forming not indicated not indicated saccharolytic not indicated not indicated not consumed not consumed not indicated not indicated not indicated not indicated not indicated -Carboxydothermus siderophilus 10.1099/ijs.0.000620-0 anaerobe (unspecified) rod/ bacilli non-motile non-spore forming Gram-positive not indicated mixed not indicated not indicated not consumed not consumed not indicated not indicated not indicated not indicated not indicated -Desulfosporosinus auripigmenti 10.1099/ijs.0.02526-0 anaerobe (unspecified) slightly curved rods non-motile non-spore forming not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Desulfosporosinus burensis 10.1099/ijs.0.035238-0 anaerobe (unspecified) slightly curved rods non-motile spore forming Gram-negative not indicated not indicated not indicated not indicated minor product major product minor product not consumed not indicated not indicated not indicated -Desulfosporosinus hippei 10.1099/ijs.0.65368-0 anaerobe (unspecified) slightly curved rods motile spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated not consumed not consumed not indicated not indicated not indicated not indicated -Desulfosporosinus lacus 10.1099/ijs.0.63610-0 anaerobe (unspecified) rod/ bacilli not indicated spore forming Gram-negative not indicated not indicated not indicated catalase negative consumed not consumed not consumed consumed not indicated not indicated not indicated -Desulfosporosinus meridiei 10.1099/00207713-51-1-133 anaerobe (unspecified) slightly curved rods motile spore forming Gram-variable not indicated not indicated not indicated not indicated consumed not consumed not consumed consumed not indicated not consumed not indicated -Desulfosporosinus youngiae 10.1099/ijs.0.007336-0 anaerobe (unspecified) slightly curved rods not indicated spore forming Gram-variable not indicated not indicated not indicated not indicated consumed not indicated not indicated not indicated not indicated not indicated not indicated -Pelotomaculum thermopropionicum 10.1099/00207713-52-5-1729 obligate anaerobe slightly curved rods non-motile spore forming Gram-variable not indicated not indicated not indicated not indicated not indicated not indicated consumed not indicated not indicated not indicated not indicated -Pelotomaculum propionicicum 10.1099/ijs.0.64925-0 obligate anaerobe slightly curved rods non-motile spore forming Gram-positive not indicated not indicated not indicated not indicated not indicated not indicated consumed not indicated not indicated not indicated not indicated -Pelotomaculum schinkii 10.1099/ijs.0.02880-0 obligate anaerobe rod/ bacilli non-motile spore forming Gram-positive not indicated not indicated not indicated not indicated not indicated not indicated consumed not indicated not indicated not indicated not indicated -Prevotella melaninogenica 10.1099/00207713-32-4-399 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated not indicated not indicated not indicated major product major product not indicated not indicated minor product not indicated minor product -Desulfotomaculum arcticum 10.1099/ijs.0.64058-0 obligate anaerobe rod/ bacilli not indicated spore forming not indicated not indicated not indicated not indicated not indicated major product not indicated major product major product not indicated not indicated not indicated -Desulfotomaculum carboxydivorans 10.1099/ijs.0.63780-0 not indicated rod/ bacilli motile spore forming not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Desulfotomaculum defluvii 10.1099/ijs.0.047662-0 obligate anaerobe rod/ bacilli not indicated spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Desulfotomaculum ferrireducens 10.1099/ijsem.0.001139 obligate anaerobe rod/ bacilli motile spore forming Gram-positive not indicated saccharolytic not indicated not indicated consumed consumed not indicated not indicated not indicated not indicated not indicated -Desulfotomaculum gibsoniae 10.1099/00207713-49-4-1801 obligate anaerobe rods or slightly curved rods motile spore forming Gram-negative not indicated not indicated not indicated not indicated consumed not indicated consumed consumed major product consumed not indicated -Desulfotomaculum halophilum 10.1099/00207713-48-2-333 obligate anaerobe rods or curved rods motile spore forming not indicated not indicated not indicated not indicated not indicated consumed not indicated not indicated not indicated not indicated not indicated not indicated -Desulfotomaculum hydrothermale 10.1099/ijs.0.65339-0 anaerobe (unspecified) slightly curved rods motile spore forming Gram-negative not indicated not indicated not indicated not indicated consumed major product not indicated not indicated not indicated not indicated not indicated -Desulfotomaculum intricatum 10.1099/ijs.0.051854-0 not indicated rod/ bacilli motile not indicated Gram-variable not indicated asaccharolytic not indicated not indicated consumed consumed not indicated consumed not indicated not indicated not indicated -Desulfotomaculum luciae 10.1099/00207713-47-3-615 obligate anaerobe rod/ bacilli motile spore forming not indicated not indicated asaccharolytic not indicated not indicated consumed not consumed not indicated not indicated not indicated not indicated not indicated -Desulfotomaculum nigrificans N/A anaerobe (unspecified) rod/ bacilli motile spore forming Gram-negative not indicated asaccharolytic http://mmbr.asm.org/content/29/3/359.full.pdf+html not indicated not indicated not consumed not consumed not indicated not indicated not indicated not indicated not indicated -Desulfotomaculum orientis N/A anaerobe (unspecified) curved rods motile spore forming Gram-negative not indicated asaccharolytic http://mmbr.asm.org/content/29/3/359.full.pdf+html not indicated not indicated not consumed not consumed not indicated not indicated not indicated not indicated not indicated -Desulfotomaculum peckii 10.1099/ijs.0.043893-0 obligate anaerobe slightly curved rods non-motile spore forming Gram-positive not indicated asaccharolytic not indicated not indicated not consumed major product major product major product not indicated not indicated not indicated -Desulfotomaculum putei 10.1099/00207713-47-3-615 obligate anaerobe rod/ bacilli motile spore forming not indicated not indicated saccharolytic not indicated not indicated consumed not consumed not indicated not indicated not indicated not indicated not indicated -Desulfotomaculum reducens 10.1099/ijsem.0.000786 not indicated slightly curved rods motile spore forming not indicated not indicated saccharolytic not indicated not indicated consumed major product consumed consumed not indicated consumed not indicated -Desulfotomaculum ruminis N/A anaerobe (unspecified) rod/ bacilli motile spore forming Gram-negative not indicated asaccharolytic http://mmbr.asm.org/content/29/3/359.full.pdf+html not indicated not indicated consumed not consumed not indicated not indicated not indicated not indicated not indicated -Desulfotomaculum solfataricum 10.1099/ijs.0.02476-0 not indicated rod/ bacilli not indicated spore forming Gram-negative not indicated saccharolytic not indicated not indicated consumed consumed consumed consumed not indicated not indicated not indicated -Desulfotomaculum thermosapovorans 10.1099/00207713-45-2-218 not indicated rod/ bacilli motile spore forming not indicated not indicated not indicated not indicated not indicated consumed major product not consumed consumed not indicated consumed not indicated -Desulfotomaculum thermosubterraneum 10.1099/ijs.0.64439-0 not indicated rod/ bacilli motile spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Peptostreptococcus asaccharolyticus 10.1099/00207713-33-4-683 not indicated not indicated not indicated not indicated not indicated not indicated mixed urease negative catalase variable not indicated major product minor product major product not producted not indicated not producted -Peptostreptococcus harei 10.1099/00207713-47-3-781 obligate anaerobe cocci not indicated not indicated Gram-positive not indicated mixed urease negative catalase variable not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Peptostreptococcus heliotrinreducens 10.1099/00207713-36-1-107 anaerobe (unspecified) cocci not indicated not indicated not indicated not indicated asaccharolytic urease negative not indicated not indicated major product not indicated minor product not indicated not indicated major product -Peptostreptococcus hydrogenalis 10.1099/00207713-40-3-305 obligate anaerobe cocci not indicated not indicated Gram-positive not indicated saccharolytic not indicated catalase variable not indicated major product not indicated major product not indicated not indicated not indicated -Peptostreptococcus indolicus 10.1099/00207713-33-4-683 not indicated not indicated not indicated not indicated not indicated not indicated asaccharolytic urease negative catalase negative not indicated major product major product major product not indicated not indicated not indicated -Peptostreptococcus ivorii 10.1099/00207713-47-3-781 obligate anaerobe cocci not indicated not indicated Gram-positive not indicated asaccharolytic urease negative catalase variable not indicated minor product minor product major product minor product minor product major product -Peptostreptococcus lacrimalis 10.1099/00207713-42-4-602 obligate anaerobe cocci not indicated not indicated Gram-positive not indicated asaccharolytic urease negative not indicated not indicated major product not indicated major product not indicated not indicated not indicated -Peptostreptococcus lactolyticus 10.1099/00207713-42-4-602 obligate anaerobe cocci not indicated not indicated Gram-positive not indicated saccharolytic urease positive not indicated not indicated major product not indicated major product not indicated not indicated not indicated -Peptostreptococcus magnus 10.1099/00207713-33-4-683 not indicated not indicated not indicated not indicated not indicated not indicated not indicated urease negative catalase variable not indicated major product not indicated not producted not indicated not indicated not indicated -Peptostreptococcus octavius 10.1099/00207713-47-3-781 obligate anaerobe cocci not indicated not indicated Gram-positive not indicated saccharolytic urease negative catalase variable not indicated not indicated not indicated major product not indicated not indicated major product -Peptostreptococcus prevotii 10.1099/00207713-33-4-683 not indicated not indicated not indicated not indicated not indicated not indicated mixed not indicated catalase variable not indicated major product minor product major product not indicated not indicated not indicated -Peptostreptococcus russellii 10.1099/ijs.0.023762-0 obligate anaerobe cocci non-motile not indicated Gram-positive not indicated saccharolytic urease negative catalase negative minor product major product not indicated not indicated not indicated not indicated not indicated -Peptostreptococcus tetradius 10.1099/00207713-33-4-683 obligate anaerobe not indicated not indicated not indicated not indicated not indicated saccharolytic urease positive catalase variable not indicated not indicated not indicated major product not indicated not indicated not indicated -Peptostreptococcus vaginalis 10.1099/00207713-42-4-602 obligate anaerobe cocci not indicated not indicated Gram-positive not indicated saccharolytic urease negative not indicated not indicated major product not indicated major product not indicated not indicated not indicated -Lachnoanaerobaculum orale 10.1099/ijs.0.033613-0 obligate anaerobe rod/ bacilli not indicated spore forming Gram-variable not indicated saccharolytic urease positive not indicated not indicated major product not indicated major product not indicated not indicated not indicated -Lachnoanaerobaculum saburreum 10.1099/ijs.0.033613-0 obligate anaerobe rod/ bacilli not indicated spore forming Gram-variable not indicated saccharolytic not indicated not indicated not indicated major product not indicated major product not indicated not indicated not indicated -Lachnoanaerobaculum umeaense 10.1099/ijs.0.033613-0 obligate anaerobe rod/ bacilli not indicated spore forming Gram-variable not indicated saccharolytic urease positive not indicated not indicated major product not indicated major product not indicated not indicated not indicated -Helcococcus kunzii 10.1099/00207713-43-3-425 facultative anaerobe not indicated non-motile not indicated not indicated no growth in 20% bile saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helcococcus ovis 10.1099/00207713-49-4-1429 facultative anaerobe cocci non-motile not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Helcococcus sueciensis 10.1099/ijs.0.63077-0 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Stomatobaculum longum 10.1099/ijs.0.042812-0 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-variable not indicated saccharolytic urease negative catalase negative not indicated major product not indicated major product not indicated not indicated major product -Abyssivirga alkaniphila 10.1099/ijsem.0.000934 obligate anaerobe rod/ bacilli motile non-spore forming not indicated not indicated saccharolytic not indicated not indicated not consumed not producted not indicated not indicated not indicated not indicated not indicated -Cellulosilyticum lentocellum 10.1099/ijs.0.014712-0 obligate anaerobe slightly curved rods motile spore forming Gram-negative growth in 20% bile saccharolytic urease positive catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Cellulosilyticum ruminicola 10.1099/ijs.0.014712-0 obligate anaerobe rods or slightly curved rods non-motile spore forming Gram-variable not indicated saccharolytic urease negative catalase negative major product major product not indicated not producted not indicated not indicated not indicated -Mobilitalea sibirica 10.1099/ijs.0.057109-0 not indicated rod/ bacilli not indicated not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Pelospora glutarica 10.1099/00207713-50-2-645 not indicated rod/ bacilli motile spore forming Gram-negative not indicated asaccharolytic not indicated not indicated not indicated not indicated major product major product major product not indicated not indicated -Pseudoramibacter alactolyticus 10.1099/00207713-46-4-1083 not indicated not indicated not indicated not indicated not indicated no growth in 20% bile saccharolytic not indicated not indicated major product major product consumed major product not indicated major product not indicated -Robinsoniella peoriensis 10.1099/ijs.0.65676-0 anaerobe (unspecified) rods or oval-shaped not indicated spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated major product not indicated not producted not indicated not indicated not indicated -Sporobacterium olearium 10.1099/00207713-49-4-1741 obligate anaerobe slightly curved rods motile spore forming Gram-positive not indicated asaccharolytic not indicated not indicated not consumed major product not indicated major product not indicated not indicated not indicated -Syntrophomonas cellicola 10.1099/ijs.0.64377-0 not indicated slightly curved rods motile spore forming Gram-variable not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Syntrophomonas curvata 10.1099/ijs.0.02903-0 not indicated curved rods motile non-spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated major product major product not indicated major product not indicated major product -Syntrophomonas erecta 10.1099/ijs.0.63372-0 not indicated rod/ bacilli not indicated non-spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated major product major product not indicated not consumed not indicated not consumed -Syntrophomonas palmitatica 10.1099/ijs.0.64981-0 obligate anaerobe slightly curved rods not indicated not indicated Gram-negative not indicated not indicated not indicated not indicated not indicated not consumed not consumed not indicated not consumed not indicated not indicated -Syntrophomonas zehnderi 10.1099/ijs.0.64734-0 not indicated slightly curved rods motile spore forming Gram-variable not indicated not indicated not indicated not indicated consumed major product major product not indicated not consumed not indicated not consumed -Syntrophothermus lipocalidus 10.1099/00207713-50-2-771 not indicated slightly curved rods motile non-spore forming not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated major product consumed not indicated not indicated -Thermosyntropha lipolytica 10.1099/00207713-46-4-1131 not indicated rods or slightly curved rods non-motile non-spore forming not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated consumed not indicated not indicated not indicated -Thermosyntropha tengcongensis 10.1099/ijs.0.033456-0 not indicated slightly curved rods non-motile non-spore forming Gram-negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Tissierella creatinini 10.1099/00207713-45-3-436 anaerobe (unspecified) rod/ bacilli non-motile non-spore forming Gram-positive not indicated asaccharolytic urease negative not indicated consumed major product not indicated not indicated not indicated not indicated not indicated -Tissierella creatinophila 10.1099/00207713-48-3-983 anaerobe (unspecified) rod/ bacilli motile not indicated Gram-positive not indicated not indicated not indicated not indicated consumed major product not indicated major product not indicated not indicated not indicated -Tissierella praeacuta 10.1099/00207713-36-3-461 not indicated not indicated motile not indicated not indicated not indicated saccharolytic urease negative not indicated not indicated major product minor product major product minor product not indicated major product -Parasutterella secunda 10.1099/ijs.0.023556-0 obligate anaerobe cocci or oval-shaped non-motile non-spore forming Gram-negative not indicated asaccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Olivibacter ginsengisoli 10.1099/ijs.0.65299-0 not indicated not indicated not indicated not indicated not indicated not indicated asaccharolytic urease positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Olivibacter jilunii 10.1099/ijs.0.042416-0 aerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Olivibacter oleidegradans 10.1099/ijs.0.026641-0 obligate anaerobe rod/ bacilli non-motile not indicated Gram-negative not indicated not indicated urease negative catalase positive not indicated not indicated not consumed not indicated not indicated not consumed not indicated -Olivibacter soli 10.1099/ijs.0.65299-0 not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic urease positive not indicated not indicated not indicated not consumed not indicated not indicated not consumed not indicated -Olivibacter terrae 10.1099/ijs.0.65299-0 not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic urease positive not indicated not indicated not indicated not consumed not indicated not indicated not consumed not indicated -Eggerthella lenta 10.1002/9781118960608.gbm00219 not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic not indicated catalase positive not indicated major product not indicated not indicated not indicated not indicated not indicated -Eubacterium rectale 10.1002/9781118960608.gbm00629 not indicated rods or slightly curved rods variable not indicated Gram-positive no growth in 20% bile saccharolytic not indicated catalase negative not indicated major product minor product major product not indicated not indicated not indicated -Eubacterium limosum 10.1002/9781118960608.gbm00629 not indicated not indicated non-motile not indicated not indicated not indicated mixed urease negative catalase negative not indicated major product minor product major product minor product not indicated minor product -Fusobacterium nucleatum 10.1002/9781118960608.gbm00768 microaerobe or anaerobe fusiform non-motile not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Escherichia coli 10.1002/9781118960608.gbm01147 facultative anaerobe rod/ bacilli motile not indicated Gram-negative not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus crispatus 10.1002/9781118960608.gbm00604 not indicated rods or slightly curved rods not indicated not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus gasseri 10.1002/9781118960608.gbm00604 not indicated rod/ bacilli not indicated not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus murinus 10.1002/9781118960608.gbm00604 not indicated rod/ bacilli non-motile not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus reuteri 10.1002/9781118960608.gbm00604 not indicated bent rods non-motile not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus salivarius 10.1002/9781118960608.gbm00604 not indicated rod/ bacilli not indicated not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactococcus lactis 10.1002/9781118960608.gbm00610 facultative anaerobe ovoid non-motile not indicated Gram-positive growth in 20% bile saccharolytic not indicated catalase negative not indicated not indicated not consumed not indicated not indicated not indicated not indicated -Leptotrichia goodfellowii 10.1002/9781118960608.gbm00771 facultative anaerobe rods or slightly curved rods non-motile non-spore forming Gram-negative not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Neisseria gonorrhoeae 10.1002/9781118960608.gbm00981 aerobe cocci variable non-spore forming Gram-negative not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Propionibacterium acnes 10.1002/9781118960608.gbm00167 variable pleomorphic not indicated not indicated not indicated not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Pseudomonas aeruginosa 10.1002/9781118960608.gbm01210 not indicated rod/ bacilli motile not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated consumed consumed consumed consumed consumed consumed -Ralstonia pickettii 10.1002/9781118960608.gbm00941 aerobe rod/ bacilli motile not indicated Gram-negative not indicated saccharolytic urease positive catalase positive not indicated consumed not indicated not indicated not indicated not indicated not indicated -Ruminococcus flavefaciens 10.1002/9781118960608.gbm00678 obligate anaerobe cocci non-motile non-spore forming Gram-positive not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Sneathia sanguinegens 10.1002/9781118960608.gbm00773 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated saccharolytic urease negative catalase negative major product minor product not indicated not indicated not indicated not indicated not indicated -Veillonella parvula 10.1002/9781118960608.gbm00710 variable cocci non-motile non-spore forming Gram-negative not indicated mixed not indicated catalase variable not indicated major product major product not indicated not indicated not indicated not indicated -Clostridium butyricum 10.1002/9781118960608.gbm00619 not indicated rod/ bacilli motile spore forming Gram-positive not indicated saccharolytic not indicated not indicated major product major product not indicated major product not indicated not indicated not indicated -Clostridium perfringens 10.1002/9781118960608.gbm00619 not indicated rod/ bacilli non-motile mixed Gram-positive growth in 20% bile saccharolytic not indicated not indicated minor product major product major product major product not indicated not indicated minor product -Staphylococcus aureus 10.1002/9781118960608.gbm00569 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus epidermidis 10.1002/9781118960608.gbm00569 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic urease positive not indicated not indicated major product not indicated not indicated not indicated not indicated not indicated -Staphylococcus haemolyticus 10.1002/9781118960608.gbm00569 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus hyicus 10.1002/9781118960608.gbm00569 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic urease variable catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus intermedius 10.1002/9781118960608.gbm00569 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic urease positive catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Staphylococcus lentus 10.1002/9781118960608.gbm00569 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative catalase positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus anginosus 10.1002/9781118960608.gbm00612 not indicated cocci not indicated not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus gordonii 10.1002/9781118960608.gbm00612 not indicated cocci not indicated not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus mitis 10.1002/9781118960608.gbm00612 not indicated cocci not indicated not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus salivarius 10.1002/9781118960608.gbm00612 not indicated cocci or ovoid not indicated not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus sanguinis 10.1002/9781118960608.gbm00612 not indicated cocci not indicated not indicated not indicated not indicated saccharolytic urease negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Streptococcus thermophilus 10.1002/9781118960608.gbm00612 facultative anaerobe cocci or ovoid not indicated not indicated not indicated not indicated saccharolytic urease negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium actinocoloniiforme 10.1099/ijs.0.022525-0 microaerobe or anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium aesculapii 10.1099/ijs.0.056937-0 aerobe, microaerobe, or anaerobe irregular rods non-motile non-spore forming Gram-positive not indicated saccharolytic urease positive catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Bifidobacterium angulatum 10.1099/00207713-24-1-6 anaerobe (unspecified) not indicated non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product not producted not producted not indicated not indicated not indicated -Bifidobacterium aquikefiri 10.1099/ijsem.0.000877 aerobe, microaerobe, or anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative major product major product not indicated not indicated not indicated not indicated not indicated -Bifidobacterium bohemicum 10.1099/ijs.0.022525-0 obligate anaerobe irregular rods non-motile non-spore forming Gram-positive not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium bombi 10.1099/ijs.0.002915-0 obligate anaerobe irregular rods non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium boum 10.1099/00207713-29-4-291 aerotolerant irregular non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative minor product major product not producted not producted not indicated not indicated not indicated -Bifidobacterium catenulatum 10.1099/00207713-24-1-6 anaerobe (unspecified) not indicated non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Bifidobacterium choerinum 10.1099/00207713-29-4-291 anaerobe (unspecified) irregular non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative minor product major product not producted not producted not indicated not indicated not indicated -Bifidobacterium coryneforme 10.1099/00207713-32-3-358 anaerobe (unspecified) cocci, oval-shaped, or club-shaped rods not indicated not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium cuniculi 10.1099/00207713-29-4-291 anaerobe (unspecified) irregular rods non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative minor product major product not producted not producted not indicated not indicated not indicated -Bifidobacterium denticolens 10.1099/00207713-46-2-564 anaerobe (unspecified) irregular rods non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Bifidobacterium eulemuris 10.1099/ijsem.0.000924 microaerobe or anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium faecale 10.1099/ijs.0.063479-0 obligate anaerobe Y-shaped rods non-motile not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium gallicum 10.1099/00207713-40-1-100 obligate anaerobe irregular rods non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated major product major product not indicated not indicated not indicated not indicated not indicated -Bifidobacterium gallinarum 10.1099/00207713-33-2-127 obligate anaerobe slightly curved rods or club-shaped non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated not indicated not producted not producted not indicated not indicated not indicated -Bifidobacterium globosum 10.1099/00207713-32-3-358 anaerobe (unspecified) cocci, oval-shaped, or club-shaped rods not indicated not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium hapali 10.1099/ijsem.0.000708 microaerobe or anaerobe irregular rods non-motile non-spore forming Gram-positive not indicated saccharolytic urease positive catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium inopinatum 10.1099/00207713-46-2-564 anaerobe (unspecified) irregular cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Bifidobacterium kashiwanohense 10.1099/ijs.0.024521-0 anaerobe (unspecified) rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium lemurum 10.1099/ijs.0.000162 microaerobe or anaerobe spiral, ring shaped, or Y-shaped rods non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium magnum 10.1099/00207713-24-1-29 anaerobe (unspecified) irregular rods non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not producted major product not producted not producted not indicated not indicated not indicated -Bifidobacterium merycicum 10.1099/00207713-41-1-163 anaerobe (unspecified) irregular rods non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not producted not producted not indicated not indicated not indicated -Bifidobacterium minimum 10.1099/00207713-32-3-358 anaerobe (unspecified) rods, oval-shaped, or club-shaped not indicated not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium mongoliense 10.1099/ijs.0.006247-0 facultative anaerobe irregular rods non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium moukalabense 10.1099/ijs.0.055186-0 obligate anaerobe irregular rods non-motile not indicated Gram-positive not indicated saccharolytic urease negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium myosotis 10.1099/ijsem.0.000708 anaerobe (unspecified) irregular rods non-motile non-spore forming Gram-positive not indicated not indicated urease positive catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium psychraerophilum 10.1099/ijs.0.02667-0 facultative anaerobe irregular rods non-motile non-spore forming Gram-positive not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium ruminantium 10.1099/00207713-41-1-163 anaerobe (unspecified) irregular non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product not producted not producted not indicated not indicated not indicated -Bifidobacterium scardovii 10.1099/00207713-52-3-995 facultative anaerobe rods or curved rods non-motile non-spore forming Gram-positive not indicated saccharolytic urease variable catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Bifidobacterium stercoris 10.1099/ijs.0.019943-0 anaerobe (unspecified) club or Y-shaped non-motile non-spore forming Gram-positive no growth in 20% bile saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Bifidobacterium subtile 10.1099/00207713-32-3-358 anaerobe (unspecified) irregular not indicated not indicated not indicated not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium thermacidophilum 10.1099/00207713-50-1-119 anaerobe (unspecified) irregular rods non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Bifidobacterium tissieri 10.1099/ijsem.0.000708 aerobe, microaerobe, or anaerobe Y-shaped rods non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Bifidobacterium tsurumiense 10.1099/ijs.0.65296-0 facultative anaerobe rods or cocci not indicated not indicated Gram-positive not indicated saccharolytic urease negative catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Fusobacterium alocis 10.1099/00207713-35-4-475 obligate anaerobe rod/ bacilli variable non-spore forming Gram-negative not indicated not indicated urease negative catalase negative not indicated major product not indicated major product not indicated not indicated not indicated -Fusobacterium sulci 10.1099/00207713-35-4-475 obligate anaerobe rod/ bacilli non-motile non-spore forming Gram-negative not indicated not indicated urease negative catalase negative not indicated minor product not indicated major product not indicated not indicated not indicated -Fusobacterium equinum 10.1099/00207713-51-6-1959 not indicated pleomorphic rods non-motile not indicated Gram-variable growth in 20% bile not indicated not indicated not indicated not indicated major product major product major product not indicated not indicated not indicated -Fusobacterium pseudonecrophorum 10.1099/00207713-40-1-71 obligate anaerobe rod/ bacilli not indicated non-spore forming Gram-negative not indicated saccharolytic not indicated not indicated not indicated not indicated major product major product not indicated not indicated not indicated -Fusobacterium simiae 10.1099/00207713-32-2-191 anaerobe (unspecified) fusiform non-motile not indicated Gram-negative not indicated saccharolytic not indicated not indicated not indicated minor product minor product major product not producted not indicated not producted -Fusobacterium ulcerans 10.1099/00207713-38-4-447 obligate anaerobe pleomorphic rods non-motile non-spore forming Gram-negative not indicated saccharolytic urease negative catalase negative not indicated minor product minor product major product not indicated not indicated not indicated -Fusobacterium varium N/A not indicated rods, cocci, or oval-shaped not indicated not indicated not indicated not indicated saccharolytic http://jb.asm.org/content/25/4/389.full.pdf+html not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus acetotolerans 10.1099/00207713-36-4-544 facultative anaerobe rod/ bacilli not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus acidifarinae 10.1099/ijs.0.63274-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Lactobacillus acidipiscis 0.1099/00207713-50-4-1479 microaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus algidus 10.1099/00207713-50-3-1143 facultative anaerobe rods or oval-shaped non-motile non-spore forming Gram-positive not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus amylotrophicus 10.1099/ijs.0.64463-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus amylovorus 10.1099/00207713-31-1-56 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated minor product not indicated not indicated not indicated not indicated not indicated -Lactobacillus antri 10.1099/ijs.0.63083-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus apinorum 10.1099/ijs.0.059600-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus apis 10.1099/ijs.0.053033-0 microaerobe or anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not consumed not indicated not indicated not indicated not indicated -Lactobacillus aquaticus 10.1099/ijs.0.008276-0 microaerobe rod/ bacilli motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus arizonensis 10.1099/00207713-50-5-1803 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus backii 10.1099/ijs.0.051920-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus bobalius 10.1099/ijs.0.65695-0 microaerobe rod/ bacilli not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not consumed not indicated not indicated -Lactobacillus bombi 10.1099/ijs.0.063602-0 microaerobe or anaerobe curved rods not indicated not indicated Gram-positive not indicated saccharolytic urease variable catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus brantae 10.1099/ijs.0.033852-0 facultative anaerobe rods, cocci, or oval-shaped non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not consumed not consumed not consumed consumed not indicated not indicated not indicated -Lactobacillus cacaonum 10.1099/ijs.0.001172-0 facultative anaerobe rod/ bacilli non-motile not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Lactobacillus capillatus 10.1099/ijs.0.65834-0 facultative anaerobe rod/ bacilli motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus casei 10.1099/00207713-21-1-69 not indicated rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus cellobiosus N/A not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic http://jb.asm.org/content/65/6/681.full.pdf+html not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus cellobiosus N/A not indicated not indicated not indicated not indicated not indicated not indicated saccharolytic http://jb.asm.org/content/65/6/681.full.pdf+html not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus ceti 10.1099/ijs.0.65372-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated not indicated catalase negative not producted not producted not producted not producted not producted not producted not producted -Lactobacillus coleohominis 10.1099/00207713-51-6-2081 facultative anaerobe rod/ bacilli not indicated non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus composti 10.1099/ijs.0.64743-0 facultative anaerobe rod/ bacilli non-motile not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus concavus 10.1099/ijs.0.63509-0 facultative anaerobe curved rods non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus crustorum 10.1099/ijs.0.64836-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus curieae 10.1099/ijs.0.041830-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus cypricasei 10.1099/00207713-51-1-45 facultative anaerobe rod/ bacilli not indicated non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus dextrinicus 10.1099/ijs.0.65779-0 facultative anaerobe cocci non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not producted not producted not producted not producted not producted not producted not producted -Lactobacillus diolivorans 10.1099/00207713-52-2-639 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated major product not indicated not indicated not indicated not indicated -Lactobacillus durianis 10.1099/00207713-52-3-927 microaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Lactobacillus equi 10.1099/00207713-52-1-211 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus equicursoris 10.1099/ijs.0.009290-0 obligate anaerobe curved rods non-motile not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus equigenerosi 10.1099/ijs.0.65250-0 facultative anaerobe cocci or oval-shaped non-motile not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Lactobacillus fabifermentans 10.1099/ijs.0.001172-0 facultative anaerobe rod/ bacilli non-motile not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not producted not producted not producted not producted not producted not producted not producted -Lactobacillus faecis 10.1099/ijs.0.052985-0 facultative anaerobe rod/ bacilli non-motile not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus farraginis 10.1099/ijs.0.64618-0 facultative anaerobe rod/ bacilli non-motile not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Lactobacillus floricola 10.1099/ijs.0.022988-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus florum 10.1099/ijs.0.019067-0 facultative anaerobe rod/ bacilli non-motile not indicated Gram-positive not indicated saccharolytic not indicated catalase variable not indicated major product not indicated not indicated not indicated not indicated not indicated -Lactobacillus formosensis 10.1099/ijs.0.070938-0 facultative anaerobe rod/ bacilli not indicated not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus fornicalis 10.1099/00207713-50-3-1253 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus frumenti 10.1099/00207713-50-6-2127 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus fuchuensis 10.1099/00207713-52-4-1151 facultative anaerobe rods or curved rods non-motile non-spore forming Gram-positive not indicated saccharolytic urease negative catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus furfuricola 10.1099/ijs.0.063933-0 facultative anaerobe rod/ bacilli non-motile not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus futsaii 10.1099/ijs.0.030619-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus gallinarum 10.1099/00207713-42-3-487 facultative anaerobe rod/ bacilli not indicated non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus gastricus 10.1099/ijs.0.63083-0 not indicated rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus ghanensis 10.1099/ijs.0.64811-0 not indicated rod/ bacilli motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus gigeriorum 10.1099/ijs.0.028217-0 facultative anaerobe rods or slightly curved rods non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus gorillae 10.1099/ijs.0.068429-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus hammesii 10.1099/ijs.0.63311-0 aerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated major product not indicated not indicated not indicated not indicated not indicated -Lactobacillus hayakitensis 10.1099/ijs.0.65135-0 not indicated not indicated non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not producted not producted not producted not producted not producted not producted not producted -Lactobacillus heilongjiangensis 10.1099/ijs.0.053355-0 not indicated rod/ bacilli not indicated non-spore forming Gram-positive not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus helsingborgensis 10.1099/ijs.0.059600-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not producted not producted not producted not producted not producted not producted not producted -Lactobacillus hokkaidonensis 10.1099/ijs.0.047027-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus hominis 10.1099/ijs.0.036665-0 aerobe, microaerobe, or anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus hordei 10.1099/ijs.0.65584-0 facultative anaerobe rod/ bacilli non-motile not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus ingluviei 10.1099/ijs.0.02206-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated not indicated not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus intestinalis 10.1099/00207713-40-3-302 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus iwatensis 10.1099/ijs.0.051920-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus kalixensis 10.1099/ijs.0.63083-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus kefiranofaciens 10.1099/00207713-38-1-12 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus kefirgranum 10.1099/00207713-44-3-435 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus kimbladii 10.1099/ijs.0.059600-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not producted not producted not producted not producted not producted not producted not producted -Lactobacillus kimchicus 10.1099/ijs.0.017418-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus kimchiensis 10.1099/ijs.0.037572-0 not indicated rod/ bacilli not indicated not indicated Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus kimchii 10.1099/00207713-50-5-1789 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus kisonensis 10.1099/ijs.0.004689-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated -Lactobacillus kitasatonis 10.1099/ijs.0.02815-0 facultative anaerobe rod/ bacilli non-motile non-spore forming Gram-positive not indicated saccharolytic not indicated catalase negative not indicated not indicated not indicated not indicated not indicated not indicated not indicated diff --git a/data-raw/susceptibility_misc.csv b/data-raw/susceptibility_misc.csv deleted file mode 100644 index 2db4706..0000000 --- a/data-raw/susceptibility_misc.csv +++ /dev/null @@ -1,51 +0,0 @@ -taxon,rank,antibiotic,value,doi -Lactobacillus,Genus,vancomycin,resistant,10.1128/AEM.01738-18 -Leuconostoc,Genus,vancomycin,resistant,10.1053/jhin.1998.0605 -Pediococcus,Genus,vancomycin,resistant,10.1053/jhin.1998.0605 -Erysipelothrix,Genus,vancomycin,resistant,10.1053/jhin.1998.0605 -Mycoplasma,Genus,vancomycin,resistant,10.1038/nrmicro1464 -Faecalibacterium,Genus,vancomycin,susceptible,10.3389/fmicb.2017.01226 -Roseburia,Genus,vancomycin,susceptible,10.1099/00207713-33-3-618 -Enterococcus gallinarum,Species,vancomycin,resistant,10.1016/j.jiac.2018.01.001 -Enterococcus casseliflavus,Species,vancomycin,resistant,10.1016/j.jiac.2018.01.001 -Enterococcus flavescens,Species,vancomycin,resistant,10.1016/j.jiac.2018.01.001 -Escherichia coli,Species,tetracycline,resistant,10.1101/cshperspect.a025387 -Enterococcus faecalis,Species,tetracycline,resistant,10.1101/cshperspect.a025387 -Pseudomonas aeruginosa,Species,tetracycline,resistant,10.1101/cshperspect.a025387 -Staphylococcus aureus,Species,tetracycline,resistant,10.1101/cshperspect.a025387 -Stenotrophomonas maltophilia,Species,tetracycline,resistant,10.1101/cshperspect.a025387 -Pseudomonas,Genus,tetracycline,resistant,10.1101/cshperspect.a025387 -Bacteroides fragilis,Species,tetracycline,resistant,10.1101/cshperspect.a025387 -Enterobacter cloacae,Species,tetracycline,resistant,10.1101/cshperspect.a025387 -Acinetobacter baumannii,Species,tetracycline,resistant,10.1101/cshperspect.a025387 -Klebsiella pneumoniae,Species,tetracycline,resistant,10.1101/cshperspect.a025387 -Proteus mirabilis,Species,tetracycline,resistant,10.1101/cshperspect.a025387 -Serratia marcescens,Species,tetracycline,resistant,10.1101/cshperspect.a025387 -Enterobacter asburiae,Species,tetracycline,resistant,10.1128/CMR.00002-19 -Enterobacter bugandensis,Species,tetracycline,resistant,10.1128/CMR.00002-19 -Enterobacter aerogenes,Species,tetracycline,resistant,10.1128/CMR.00002-19 -Agrobacterium tumefaciens,Species,tetracycline,resistant,10.1186/1471-2164-8-15 -Bacillus anthracis,Species,tetracycline,resistant,10.1186/1471-2164-8-15 -Bacillus cereus,Species,tetracycline,resistant,10.1186/1471-2164-8-15 -Bacillus thuringiensis,Species,tetracycline,resistant,10.1186/1471-2164-8-15 -Bacteroides fragilis,Species,tetracycline,resistant,10.1186/1471-2164-8-15 -Bifidobacterium longum,Species,tetracycline,resistant,10.1186/1471-2164-8-15 -Clostridium acetobutylicum,Species,tetracycline,resistant,10.1186/1471-2164-8-15 -Clostridium perfringens,Species,tetracycline,resistant,10.1186/1471-2164-8-15 -Lactobacillus johnsonii,Species,tetracycline,resistant,10.1186/1471-2164-8-15 -Lactobacillus plantarum,Species,tetracycline,resistant,10.1186/1471-2164-8-15 -Streptococcus agalactiae,Species,tetracycline,resistant,10.1186/1471-2164-8-15 -Streptomyces avermitilis,Species,tetracycline,resistant,10.1186/1471-2164-8-15 -Streptomyces coelicolor,Species,tetracycline,resistant,10.1186/1471-2164-8-15 -Salmonella typhimurium,Species,tetracycline,resistant,10.1038/nrmicro1464 -Campylobacter jejuni,Species,tetracycline,resistant,10.1038/nrmicro1464 -Bacteroides,Genus,tetracycline,resistant,10.1128/mBio.00569-13 -Klebsiella,Genus,tetracycline,susceptible,10.1101/cshperspect.a025387 -Mycobacterium abscessus,Species,tetracycline,resistant,10.1128/AAC.00119-18 -Bacteroides,Genus,penicillin,resistant,10.3934/microbiol.2018.3.482 -Stenotrophomonas maltophilia,Species,penicillin,resistant,10.1186/s13054-019-2371-3 -Enterococcus faecalis,Species,penicillin,resistant,10.4161/viru.21282 -Enterococcus faecium,Species,penicillin,resistant,10.4161/viru.21282 -Escherichia coli,Species,penicillin,resistant,0.1016/j.ijmm.2013.02.009 -Mycoplasma,Genus,penicillin,resistant,10.1038/nrmicro1464 -Staphylococcus,Genus,aminoglycoside,susceptible,10.1136/archdischild-2015-309069 diff --git a/data-raw/taxon_phenotypes.Rmd b/data-raw/taxon_phenotypes.Rmd deleted file mode 100644 index 275ec76..0000000 --- a/data-raw/taxon_phenotypes.Rmd +++ /dev/null @@ -1,189 +0,0 @@ -# Taxon phenotypes data - -```{r message=FALSE, warning=FALSE} -library(tidyverse) -library(usethis) -``` - -## Allowed values - -```{r} -allowed_taxonomic_rank_values <- c( - "Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species") -``` - - -```{r} -allowed_aerobic_status_values <- c( - "obligate anaerobe", - "facultative anaerobe", - "aerobe", - NA) -refine_aerobic_status_values <- function (df) { - df %>% - mutate(aerobic_status = case_when( - aerobic_status == "anaerobe (unspecified)" ~ "obligate anaerobe", - # Assume that organisms filed under "microaerobe" and "microaerobe or - # anaerobe" have genes to neutralize O2 but do not carry out aerobic - # respiration - aerobic_status == "microaerobe" ~ "obligate anaerobe", - aerobic_status == "microaerobe or anaerobe" ~ "obligate anaerobe", - # Assume that organisms filed under "microaerobe or aerobe" can carry out - # aerobic respiration - aerobic_status == "microaerobe or aerobe" ~ "aerobe", - # This is a facultative anaerobe if I ever saw one - aerobic_status == "aerobe, microaerobe, or anaerobe" ~ "facultative anaerobe", - # Likewise, assume "aerotolerant" means facultative anaerobe - aerobic_status == "aerotolerant" ~ "facultative anaerobe", - # The labels "variable" and "not indicated" do not help us here; we need - # definite answers - aerobic_status == "variable" ~ NA_character_, - aerobic_status == "not indicated" ~ NA_character_, - TRUE ~ aerobic_status)) -} -``` - -```{r} -allowed_gram_stain_values <- c("Gram-positive", "Gram-negative", NA) -refine_gram_stain_values <- function (df) { - df %>% - mutate(gram_stain = case_when( - gram_stain == "Gram-variable" ~ NA_character_, - gram_stain == "not indicated" ~ NA_character_, - TRUE ~ gram_stain)) -} -``` - -## Curated database from Celeste Gaughan - -```{r message=FALSE} -phenotype_genus <- read_tsv("genera_0831.txt", na = "N/A") %>% - mutate(rank = "Genus") %>% - select(taxon = name, rank, aerobic_status, gram_stain, doi) %>% - refine_aerobic_status_values() %>% - refine_gram_stain_values() %>% - filter(!(is.na(aerobic_status) & is.na(gram_stain))) - -phenotype_genus %>% - count(aerobic_status) -phenotype_genus %>% - count(gram_stain) -``` - -```{r message=FALSE} -phenotype_species <- read_tsv("species_0831.txt", na = "N/A") %>% - mutate(rank = "Species") %>% - select(taxon = name, rank, aerobic_status, gram_stain, doi) %>% - refine_aerobic_status_values() %>% - refine_gram_stain_values() %>% - filter(!(is.na(aerobic_status) & is.na(gram_stain))) - -phenotype_species %>% - count(taxon) %>% - filter(n > 1) -phenotype_species %>% - count(aerobic_status) -phenotype_species %>% - count(gram_stain) -``` - -## Misc database - -```{r} -phenotype_misc <- read_csv("phenotype_misc.csv", show_col_types = FALSE) -``` - -## Final check - -```{r} -taxon_phenotypes <- bind_rows( - phenotype_misc, phenotype_genus, phenotype_species) -taxon_phenotypes %>% - count(rank) -taxon_phenotypes %>% - count(aerobic_status) -taxon_phenotypes %>% - count(gram_stain) -``` - -Check for duplicate rows - -```{r} -taxon_phenotypes %>% - count(taxon) %>% - filter(n > 1) -``` - -Check for expected taxonomic ranks - -```{r} -taxon_phenotypes %>% - filter(!(rank %in% allowed_taxonomic_rank_values)) -``` - -Check for unexpected aerobic status values - -```{r} -taxon_phenotypes %>% - filter(!(aerobic_status %in% allowed_aerobic_status_values)) -``` - -Check for unexpected Gram stain values - -```{r} -taxon_phenotypes %>% - filter(!(gram_stain %in% allowed_gram_stain_values)) -``` - -```{r eval=FALSE} -rank_colors <- structure( - RColorBrewer::brewer.pal(9, "GnBu")[4:9], - names = allowed_taxonomic_rank_values[2:7]) - -n_aerobic <- taxon_phenotypes %>% - filter(!is.na(aerobic_status)) %>% - count(rank, aerobic_status) %>% - mutate(aerobic_status = fct_reorder(aerobic_status, n)) %>% - rename(value = aerobic_status) %>% - mutate(count_by = "Aerobic status") - -n_gram <- taxon_phenotypes %>% - filter(!is.na(gram_stain)) %>% - count(rank, gram_stain) %>% - mutate(gram_stain = fct_reorder(gram_stain, n)) %>% - rename(value = gram_stain) %>% - mutate(count_by = "Gram stain") - -bind_rows(n_aerobic, n_gram) %>% - mutate(value = fct_reorder(value, n, .fun = sum)) %>% - mutate(rank = fct_relevel(rank, allowed_taxonomic_rank_values[2:7])) %>% - ggplot(aes(y = value, x = n, fill = rank)) + - geom_col() + - facet_grid(count_by ~ ., scales = "free_y", space = "free_y") + - scale_fill_manual(values = rank_colors) + - labs(x = "Number of taxa", y = "", fill = "") + - theme_bw() + - theme(strip.background = element_blank()) -ggsave("phenotype_counts.png", width = 8, height = 4, dpi = 300) -``` - -```{r eval=FALSE} -taxon_phenotypes %>% - count(rank) %>% - mutate(rank = fct_relevel(rank, allowed_taxonomic_rank_values[2:7])) %>% - ggplot() + - geom_col(aes(x = n, y = rank, fill = rank)) + - scale_fill_manual(values = rank_colors) + - labs(x = "Number of taxa annotated", y = "") + - theme_bw() + - theme(legend.position = "none") -ggsave("taxon_counts.png", width = 4, height = 2, dpi = 300) -``` - - -## Export - -```{r} -taxon_phenotypes <- as.data.frame(taxon_phenotypes) -usethis::use_data(taxon_phenotypes, overwrite = T) -``` diff --git a/data-raw/taxon_susceptibility.Rmd b/data-raw/taxon_susceptibility.Rmd deleted file mode 100644 index c85d177..0000000 --- a/data-raw/taxon_susceptibility.Rmd +++ /dev/null @@ -1,94 +0,0 @@ -# Antibiotic susceptibility - -```{r message=FALSE} -library(tidyverse) -library(usethis) -``` - -## Allowed values - -```{r} -allowed_taxonomic_rank_values <- c( - "Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species") -``` - -```{r} -allowed_susceptibility_values <- c("susceptible", "resistant") -``` - - -## Vancomycin - -Manually curated Lactobacillus database from abx susceptibility paper. Don't -take phenotype info from this paper. The info in table 1 indicates the -conditions under which the strain was grown for the experiment, not all -conditions under which it can be grown. There is more good info on other abx -to take from this paper. - -```{r message=FALSE} -susceptibility_lactobacillus <- read_csv( "Lactobacillus_data.csv") %>% - mutate(antibiotic = "vancomycin") %>% - select(taxon = name, rank, antibiotic, value = vancomycin, doi) %>% - mutate(taxon = str_replace_all(taxon, "\\s+", " ")) %>% - # Policy of this package is not to work with subspecies, but instead to - # convert subspecies name to an equivalent species name, and pretend the - # subspecies is just a different species. - mutate(taxon = str_remove(taxon, " \\w+ subsp\\.")) %>% - mutate(value = if_else(value, "susceptible", "resistant")) -``` - -```{r} -susceptibility_lactobacillus %>% - count(antibiotic, value) -``` - -## Other info - -```{r message=FALSE} -susceptibility_misc <- read_csv("susceptibility_misc.csv") -``` - -```{r} -susceptibility_misc %>% - count(antibiotic, value) -``` - -## Final checks - -```{r} -taxon_susceptibility <- bind_rows( - susceptibility_misc, susceptibility_lactobacillus) -taxon_susceptibility %>% - count(antibiotic, value) -``` - -Check for unexpected taxonomic rank values - -```{r} -taxon_susceptibility %>% - filter(!(rank %in% allowed_taxonomic_rank_values)) -``` - -Check for unexpected susceptibility values - -```{r} -taxon_susceptibility %>% - filter(!(value %in% allowed_susceptibility_values)) -``` - -## Export - -```{r} -taxon_susceptibility <- as.data.frame(taxon_susceptibility) -usethis::use_data(taxon_susceptibility, overwrite = T) -``` - -Review paper on drug class: -https://doi.org/10.1016/j.bcp.2017.01.003 - -Tet protection genes on mobile elements: -http://faculty.washington.edu/marilynr/ -https://doi.org/10.1016/j.femsle.2005.02.034 - -The Clinical and Laboratory Standards Institute (CLSI) guidelines assesses abx -resistance. diff --git a/data/taxon_phenotypes.rda b/data/taxon_phenotypes.rda deleted file mode 100644 index 8a0cf6d..0000000 Binary files a/data/taxon_phenotypes.rda and /dev/null differ diff --git a/data/taxon_susceptibility.rda b/data/taxon_susceptibility.rda deleted file mode 100644 index bf8fd4c..0000000 Binary files a/data/taxon_susceptibility.rda and /dev/null differ diff --git a/man/antibiotic_specific_susceptibility.Rd b/man/antibiotic_specific_susceptibility.Rd index e6eca93..05a5ae0 100644 --- a/man/antibiotic_specific_susceptibility.Rd +++ b/man/antibiotic_specific_susceptibility.Rd @@ -10,24 +10,24 @@ \usage{ antibiotic_susceptibility_vancomycin( lineage, - antibiotic_db = taxon_susceptibility, - phenotype_db = taxon_phenotypes + antibiotic_db = whatbacteria::taxon_susceptibility, + phenotype_db = whatbacteria::taxon_phenotypes ) antibiotic_susceptibility_tetracycline( lineage, - antibiotic_db = taxon_susceptibility + antibiotic_db = whatbacteria::taxon_susceptibility ) antibiotic_susceptibility_penicillin( lineage, - antibiotic_db = taxon_susceptibility + antibiotic_db = whatbacteria::taxon_susceptibility ) antibiotic_susceptibility_aminoglycoside( lineage, - antibiotic_db = taxon_susceptibility, - phenotype_db = taxon_phenotypes + antibiotic_db = whatbacteria::taxon_susceptibility, + phenotype_db = whatbacteria::taxon_phenotypes ) } \arguments{ diff --git a/man/antibiotic_susceptibility.Rd b/man/antibiotic_susceptibility.Rd index 22185fb..bfc6502 100644 --- a/man/antibiotic_susceptibility.Rd +++ b/man/antibiotic_susceptibility.Rd @@ -4,7 +4,11 @@ \alias{antibiotic_susceptibility} \title{Evaluate susceptibility based on antibiotic-specific annotations} \usage{ -antibiotic_susceptibility(lineage, antibiotic, db = taxon_susceptibility) +antibiotic_susceptibility( + lineage, + antibiotic, + db = whatbacteria::taxon_susceptibility +) } \arguments{ \item{lineage}{A character vector of taxonomic assignments or lineages} diff --git a/man/mirix_antibiotic.Rd b/man/mirix_antibiotic.Rd index 64d20f6..40f7477 100644 --- a/man/mirix_antibiotic.Rd +++ b/man/mirix_antibiotic.Rd @@ -14,44 +14,44 @@ mirix_vancomycin( abundance, lineage, replace_zero = 1e-04, - antibiotic_db = taxon_susceptibility, - phenotype_db = taxon_phenotypes + antibiotic_db = whatbacteria::taxon_susceptibility, + phenotype_db = whatbacteria::taxon_phenotypes ) mirix_doxycycline( abundance, lineage, replace_zero = 1e-04, - antibiotic_db = taxon_susceptibility + antibiotic_db = whatbacteria::taxon_susceptibility ) mirix_amoxicillin( abundance, lineage, replace_zero = 1e-04, - antibiotic_db = taxon_susceptibility + antibiotic_db = whatbacteria::taxon_susceptibility ) mirix_metronidazole( abundance, lineage, replace_zero = 1e-04, - phenotype_db = taxon_phenotypes + phenotype_db = whatbacteria::taxon_phenotypes ) mirix_ciprofloxacin( abundance, lineage, replace_zero = 1e-04, - phenotype_db = taxon_phenotypes + phenotype_db = whatbacteria::taxon_phenotypes ) mirix_gentamicin( abundance, lineage, replace_zero = 1e-04, - antibiotic_db = taxon_susceptibility, - phenotype_db = taxon_phenotypes + antibiotic_db = whatbacteria::taxon_susceptibility, + phenotype_db = whatbacteria::taxon_phenotypes ) } \arguments{ diff --git a/man/phenotype_susceptibility.Rd b/man/phenotype_susceptibility.Rd index 980d9fa..9e7cc0f 100644 --- a/man/phenotype_susceptibility.Rd +++ b/man/phenotype_susceptibility.Rd @@ -8,7 +8,7 @@ phenotype_susceptibility( lineage, phenotype, susceptibility, - db = taxon_phenotypes + db = whatbacteria::taxon_phenotypes ) } \arguments{ diff --git a/man/predict_abundance.Rd b/man/predict_abundance.Rd index ebb2573..60913d5 100644 --- a/man/predict_abundance.Rd +++ b/man/predict_abundance.Rd @@ -9,10 +9,10 @@ predict_abundance(index_value, abundance, susceptibility) \arguments{ \item{index_value}{Value or values of the index at which to make predictions.} +\item{abundance}{A vector of taxon abundances in a sample.} + \item{susceptibility}{A character vector of antibiotic susceptibility, with values that are "susceptible", "resistant", or \code{NA}.} - -\item{abundances}{A vector of taxon abundances in a sample.} } \value{ A new vector of abundances if \code{index_value} has length 1. If diff --git a/man/taxon_phenotypes.Rd b/man/taxon_phenotypes.Rd deleted file mode 100644 index a9594e9..0000000 --- a/man/taxon_phenotypes.Rd +++ /dev/null @@ -1,27 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{taxon_phenotypes} -\alias{taxon_phenotypes} -\title{Gram stain and aerobic status of bacterial taxa} -\format{ -A data frame with the following columns: -\describe{ -\item{taxon}{The name of the taxon} -\item{rank}{The rank of the taxon} -\item{aerobic_status}{ -The aerobic status. One of "aerobe", "facultative anaerobe", or -"obligate anaerobe".} -\item{gram_stain}{ -How the taxon appears when Gram-stained. One of "Gram-positive" or -"Gram-negative".} -\item{doi}{DOI of the publication from which the information was obtained.} -} -} -\usage{ -taxon_phenotypes -} -\description{ -Gram stain and aerobic status of bacterial taxa -} -\keyword{datasets} diff --git a/man/taxon_susceptibility.Rd b/man/taxon_susceptibility.Rd deleted file mode 100644 index f570425..0000000 --- a/man/taxon_susceptibility.Rd +++ /dev/null @@ -1,25 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/data.R -\docType{data} -\name{taxon_susceptibility} -\alias{taxon_susceptibility} -\title{Antibiotic susceptibility of bacterial taxa} -\format{ -A data frame with the following columns: -\describe{ -\item{taxon}{The name of the taxon} -\item{rank}{The rank of the taxon} -\item{antibiotic}{The antibiotic or antibiotic class} -\item{value}{ -The susceptibility of the taxon to the antibiotic, one of "susceptible" -or "resistant".} -\item{doi}{DOI of the publication from which the information was obtained.} -} -} -\usage{ -taxon_susceptibility -} -\description{ -Antibiotic susceptibility of bacterial taxa -} -\keyword{datasets} diff --git a/mirix.Rproj b/mirix.Rproj index 6f84630..91af0bd 100644 --- a/mirix.Rproj +++ b/mirix.Rproj @@ -1,23 +1,23 @@ -Version: 1.0 - -RestoreWorkspace: No -SaveWorkspace: No -AlwaysSaveHistory: Default - -EnableCodeIndexing: Yes -UseSpacesForTab: Yes -NumSpacesForTab: 2 -Encoding: UTF-8 - -RnwWeave: Sweave -LaTeX: pdfLaTeX - -AutoAppendNewline: Yes -StripTrailingWhitespace: Yes -LineEndingConversion: Posix - -BuildType: Package -PackageUseDevtools: Yes -PackageInstallArgs: --no-multiarch --with-keep.source -PackageCheckArgs: --as-cran -PackageRoxygenize: rd,collate,namespace,vignette +Version: 1.0 + +RestoreWorkspace: No +SaveWorkspace: No +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX + +AutoAppendNewline: Yes +StripTrailingWhitespace: Yes +LineEndingConversion: Posix + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source +PackageCheckArgs: --as-cran +PackageRoxygenize: rd,collate,namespace,vignette diff --git a/tests/testthat/test-match.R b/tests/testthat/test-match.R deleted file mode 100644 index 131ad06..0000000 --- a/tests/testthat/test-match.R +++ /dev/null @@ -1,203 +0,0 @@ -gram_stain_db <- data.frame( - taxon = c( - "Actinobacteria", "Bacteroidetes", "Firmicutes", - "Negativicutes", "Proteobacteria"), - rank = c("Phylum", "Phylum", "Phylum", "Class", "Phylum"), - value = c( - "Gram-positive", "Gram-negative", "Gram-positive", - "Gram-negative", "Gram-negative"), - stringsAsFactors = FALSE) - -vanco_db <- data.frame( - taxon = c( - "Lactobacillus", "Enterococcus flavescens", "Lactobacillus delbrueckii", - "Lactobacillus lactis", "Lactobacillus casei"), - rank = c("Genus", "Species", "Species", "Species", "Species"), - value = c( - "resistant", "resistant", "susceptible", "susceptible", "resistant"), - antibiotic = "vancomycin", - stringsAsFactors = FALSE) - -tetra_db <- data.frame( - taxon = c("Escherichia coli", "Enterococcus faecalis", "Klebsiella"), - rank = c("Species", "Species", "Genus"), - value = c("resistant", "resistant", "susceptible"), - antibiotic = "tetracycline", - stringsAsFactors = FALSE) - -test_that("antibiotic_susceptibility works for vancomycin data", { - expect_equal( - antibiotic_susceptibility( - c("Enterococcus faecalis", - "Lactobacillus", - "Lactobacillus delbrueckii"), - "vancomycin", db = vanco_db), - c(NA, "resistant", "susceptible")) -}) - -test_that("antibiotic_susceptibility works for tetracycline data", { - expect_equal( - antibiotic_susceptibility( - c("Enterococcus faecalis", - "Lactobacillus", - "Lactobacillus delbrueckii"), - "tetracycline", db = tetra_db), - c("resistant", NA, NA)) -}) - -test_that("antibiotic_susceptibility works for multi-abx data", { - mixed_db <- rbind(vanco_db, tetra_db) - expect_equal( - antibiotic_susceptibility( - c("Enterococcus faecalis", - "Lactobacillus", - "Lactobacillus delbrueckii"), - "vancomycin", db = mixed_db), - c(NA, "resistant", "susceptible")) - expect_equal( - antibiotic_susceptibility( - c("Enterococcus faecalis", - "Lactobacillus", - "Lactobacillus delbrueckii"), - "tetracycline", db = mixed_db), - c("resistant", NA, NA)) -}) - -test_that("phenotype_susceptibility works for normal input", { - pheno_db <- gram_stain_db - colnames(pheno_db)[3] <- "gram_stain" - - expect_equal( - phenotype_susceptibility( - c("Bacteroidetes", "Firmicutes", "Firmicutes Negativicutes"), - "gram_stain", - c("Gram-positive" = "susceptible", "Gram-negative" = "resistant"), - pheno_db), - c("resistant", "susceptible", "resistant")) -}) - -test_that("match_annotation works for normal input", { - # For the lineage "Firmicutes Negativicutes", the phenotype value for - # Negativicutes (Gram-negative) should override the value for Firmicutes - # (Gram-positive) - expect_equal( - match_annotation( - c("Bacteroidetes", "Firmicutes", "Firmicutes Negativicutes"), - gram_stain_db), - c("Gram-negative", "Gram-positive", "Gram-negative")) -}) - -test_that("match_annotation works for lineage of length 1", { - expect_equal( - match_annotation("Bacteroidetes", gram_stain_db), - "Gram-negative") -}) - -test_that("match_annotation works for empty lineage vector", { - expect_equal(match_annotation(character(), gram_stain_db), character()) -}) - -test_that("match_annotation works for database of length 1", { - expect_equal( - match_annotation( - c("Bacteroidetes", "Firmicutes", "Firmicutes Negativicutes"), - gram_stain_db[2,]), - c("Gram-negative", NA, NA)) -}) - -test_that("match_annotation works for empty database", { - expect_equal( - match_annotation( - c("Bacteroidetes", "Firmicutes", "Firmicutes Negativicutes"), - gram_stain_db[integer(),]), - as.character(c(NA, NA, NA))) -}) - -test_that("first_non_na_value works for multiple non-NA values", { - expect_equal(first_non_na_value(c(NA, NA, "a", NA, "b", NA)), "a") -}) - -test_that("first_non_na_value returns NA if all values are NA", { - na_chars <- as.character(c(NA, NA, NA, NA)) - expect_equal(first_non_na_value(na_chars), NA_character_) -}) - -test_that("match_taxa works for normal input", { - expect_equal( - match_taxa( - c("Bacteroidetes; hgj", "Bacteria - Firmicutes", "kgj", "jasfdljh"), - c("Firmicutes", "Bacteroidetes", "Proteobacteria")), - c(2, 1, NA, NA)) -}) - -test_that("match_taxa works for taxa with prefixes", { - prefix_lineage <- c( - "p__Bacteroidetes; hgj", - "k__Bacteria - p__Firmicutes", - "g__kgj", - "s__jasfdljh") - taxa <- c("Firmicutes", "Bacteroidetes", "Proteobacteria") - expect_equal( - match_taxa(prefix_lineage, taxa), - c(2, 1, NA, NA)) -}) - -test_that("match_taxa works for species names", { - species_lineage <- c( - "Bacteroidetes - Bacteroides vulgatus", - "Enterobacteriaceae; Escherichia; Escherichia coli", - "kgj vulgatus", - "Bacteroidetes - Bacteroides") - species_taxa <- c( - "Escherichia coli", - "Bacteroides vulgatus") - expect_equal( - match_taxa(species_lineage, species_taxa), - c(2, 1, NA, NA)) -}) - -test_that("match_taxa works for lineage vectors of length 1", { - expect_equal( - match_taxa( - "Bacteroidetes; hgj", - c("Firmicutes", "Bacteroidetes", "Proteobacteria")), - 2) -}) - -test_that("match_taxa works for taxa vectors of length 1", { - expect_equal( - match_taxa( - c("Bacteroidetes; hgj", "Bacteria - Firmicutes", "kgj", "jasfdljh"), - "Firmicutes"), - c(NA, 1, NA, NA)) -}) - -test_that("match_taxa works for empty lineage vectors", { - expect_equal( - match_taxa( - character(), - c("Firmicutes", "Bacteroidetes", "Proteobacteria")), - integer()) -}) - -test_that("match_taxa works for empty taxa vectors", { - expect_equal( - match_taxa( - c("Bacteroidetes; hgj", "Bacteria - Firmicutes", "kgj", "jasfdljh"), - character()), - as.character(c(NA, NA, NA, NA))) -}) - -test_that("match_taxa gives a warning if more than one taxon is matched", { - expect_warning(match_taxa( - c("Bacteroidetes hfg", "Firmicutes"), - c("Bacteroidetes", "Bacteroidetes hfg"))) -}) - -test_that("first_true_index works for multiple TRUE values", { - expect_equal(first_true_idx(c(FALSE, TRUE, TRUE)), 2) -}) - -test_that("first_true_index returns NA if there are no TRUE values", { - expect_equal(first_true_idx(c(FALSE, FALSE, FALSE)), NA_integer_) -}) diff --git a/tools/readme/weiss_healthy6-1.png b/tools/readme/weiss_healthy6-1.png index 91c9822..aa67b00 100644 Binary files a/tools/readme/weiss_healthy6-1.png and b/tools/readme/weiss_healthy6-1.png differ diff --git a/tools/readme/weiss_healthy6_prediction-1.png b/tools/readme/weiss_healthy6_prediction-1.png index 346b550..0c266b4 100644 Binary files a/tools/readme/weiss_healthy6_prediction-1.png and b/tools/readme/weiss_healthy6_prediction-1.png differ diff --git a/tools/readme/weiss_vancomycin_index-1.png b/tools/readme/weiss_vancomycin_index-1.png index 9b26977..f205566 100644 Binary files a/tools/readme/weiss_vancomycin_index-1.png and b/tools/readme/weiss_vancomycin_index-1.png differ