Computational modeling of microbial communities applied to D. pigrum and S. aureus in the human nose

This repository introduces the codes applied to the nasal microbial community of the latest available curated GEMs of D. pigrum and S. aureus.

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A metabolic modeling community of organisms D. pigrum and S. aureus in a nasal medium. This implements functionality to analyze the interaction between these two species within a human nose using different approaches to construct a community.

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Authors: Reihaneh Mostolizadeh, Manuel Glöckler

To run it as a package, refer to:

Repository: https://github.com/manuelgloeckler/ncmw

Full documentaion page: https://manuelgloeckler.github.io/ncmw/

► Getting started with this repository

Operating systems: MacOS, Windows, Linux.

All codes can be run separately in the jupyter notebook.

The package depends on third-party software that was successfully tested using Python (version 3.7 or later), COBRApy (version 0.19.0 or later), CPLEX (version 20.1.0). Alternativiely, other solvers for linear programing may be used as long as those are supported by COBRApy.

Overview

The repository has contained a folder named "Models," including models used in this work, a folder named "Media" including synthetic nasal medium (SNM3) used in this work and all other media created as a subset of SNM3, and all codes applied for the analysis in the related manuscript.

Model_Summary

• DP_SA_summatymodel_1: gives an overview of both models used in this research
• flux_distribution_SA: is an overview of flux distribution of S. aureus
• flux_distribution_DP is an overview of flux distribution of D. pigrum
• creat_compm_media the COMPM media was created

Similarity

• jaccard_index: which computed the similarity between both species
• uptake_sekeration_inverstigation: compare the similarity between both species from the perspective of uptake and secretion metabolites

Community

• number_12 the analysis of the community based on the pooled approaches

• number_13 the analysis of the community based on the integrated approaches while we have media SNM3, exchange, COMPM

• number_14 the analysis of the community based on the shuttle approaches while we have media SNM3, exchange, COMPM (shuttle environment was considered as all 111 total exchange reactions)- linear combination of the objective function was implemented.

• number_16 the analysis of the community based on the shuttle approaches while we have media SNM3, exchange, COMPM (shuttle environment was considered as all 111 total exchange reactions)- the convex combination of the objective function was implemented.

• number_18 the analysis of the community based on the shuttle approaches while we have media SNM3, exchange, COMPM (shuttle environment was considered as all uptake and secreted metabolites)- linear combination of the objective function and convex combination were implemented.

• numbers_20-21-22-23-24-25 computing the COOPM media in different scenarios and the analysis of the community in COOPM in all different conditions.

• numbers_26-28 a brief analysis of different scenarios while the community was created as a package to be called.

• optcom_comparison MICOM package by using otpcom objective function and the modification based on the nasal microbiom community.

☮ Licensing and distribution

The University of Tübingen, Germany