MMB-901 Microbial metagenomics

1. General introduction
2. Before the course
3. Schedule
4. Target group
5. Learning outcomes
6. Organizers and teachers

General introduction

In metagenomics all genetic material (DNA) in a sample matrix is sequenced and analyzed. Culture-dependent methods have obvious biases in microbial ecology, while uncultured taxa comprise a large fraction of microbial communities in complex ecosystems. For this reason, metagenomics has become a widely used tool for the analysis of microbial communities. Metagenomics has also many benefits compared to amplicon sequencing, as it gives information not only on the taxonomic diversity but also on the functional composition of microbial communities. Recent bioinformatic developments now allow the recovery of metagenome-assembled genomes (MAGs) at an incredible depth.

During this course the students will learn state-of-the-art bioinformatic approaches to analyse metagenomic data. The course covers both read-based and assembly-based methods, focusing on the strenght of each of these methods depending on the research question. Short-read sequencing technologies are still commonly used in metagenomics, but recent technical advances in long-read sequencing technologies are making long-read sequencing a valid option in metagenomics. Data originating from both short- (e.g. Illumina) and long-read (e.g. Nanopore/PacBio) sequencing platforms will be used in this course to demonstrate their advantages and disadvantages in metagenomics and microbial ecology.

Many things are possible thanks to the support from CSC.

Before the course

Go to myCSC and join the course project (MMB-901). Link has been sent by email and can be found from Moodle.

Compulsory prerequisites:

• Basic knowledge of UNIX
• Basic knowledge of bioinformatics, molecular biosciences and microbiology
• Bachelor's degree completed

Recommended prerequisites:

• Basic knowledge of R programming language

Schedule

The course will be from Monday 11th of November to Friday 15th of December at Viikki Campus.

Practicals:

Day	Time	Building	Class room
Monday 25.11.	10.15-15.45	🏫 Infocenter	K1046
Wednesday 27.11.	10.15-15.45	🏢 Biocenter 1	1401.4
Friday 29.11.	10.15-15.45	🏢 Biocenter 1	1401.4
Monday 2.12.	10.15-15.45	🏫 Infocenter	K1048
Wednesday 4.12.	10.15-15.45	🏢 Biocenter 1	1041.4
Thursday 5.12.	10.15-15.45	🏢 Biocenter 1	1401.4
Monday 9.12.	10.15-15.45	🏫 Infocenter	K1046
Wednesday 11.12.	10.15-15.45	🏢 Biocenter 1	1401.4
Friday 13.12.	10.15-15.45	🏢 Biocenter 1	1401.4

-- Detailed SCHEDULE --
-- Link to PRACTICALS --

Target group

This course is targeted to students from master's programme in microbiology and microbial biotechnology (MMB).

Learning outcomes

By completing this course, you will:

• Have a basic understanding of metagenomic sequencing technologies and bioinformatic approaches to analyse metagenomic data
• Be able to plan and execute a metagenomic sequencing project depending on the research questions.
• Have an up-to-date knowledge on the bioinformatic tools and best practices for the analysis of metagenomes.
• Be able to choose and critically evaluate new tools and approaches for specific research question
• Have confidence to learn and implement new bioinformatic methods using available documentation

Organizers and teachers

👨‍💻 Antti Karkman, University of Helsinki
👨‍💻 Frillix Brocks, University of Helsinki