Overview of Microbial Metagenomics


This lesson is for people who are interested in learning about why you might want to and how to study microbial communities using genomic data. This lesson assumes some knowledge of how to use the command line.

Lesson Overview

When we think about natural systems, one thing to consider are the microbes! Microbes influence everything from biogeochemical cycling to insect behavior. While previously it was challenging to get a survey of what microbes lived where, with the development of cheap genomic sequencing, we now can use genomic approaches to survey what microbes are there, how they change and even some of what they’re capable of doing in an environment.

In this lesson we’ll go through an introduction and example of the role of microbes in the environment, what sequencing is, learn about the genomic data file types and how to start processing genomic data.

Learning objectives

Lesson Outline

I. Overview of the awesomeness of microbes and how we can use metagenomics to study them

Goals: Introduce the role and importance of microbes in systems, using an example from soil microbial communities in agricultural systems and their impact on greenhouse gas fluxes. Describe how we can use genomic data to study microbial systems - amplicon (16S) and shotgun metagenomics.

Materials: Lecture slides

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II. Using cloud computing for fun and genomic data

Goals: Discuss needs for cloud computing and what are some options. Connect to Amazon AWS resources using ssh. Provide documentation on how to get access to cloud computing resources.

Materials: Introduction to cloud computing

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III. The genomic data file type and the command line

Goals: Work with the FASTQ file type at the command line.


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IV. Running bioinformatics programs

Goals: How to run bioinformatics programs at the command line, using FastQC as an example.

Materials: Bioinformatics programs - quality control

Other Resources