Microbiome & Metagenomics

Metagenomics is the study of microbial communities in their original living places. Metagenome sequencing refers to sequencing the entire genomes of all microbes present in a sample in order to explore taxonomic, functional, and evolutionary aspects.

Metagenomics is microbial community genomics

What is a microbiome?

    • the complete set of microbes that live in a particular microbial ecosystem: within and on the human body (human microbiome), specific plants (grapevine microbiome), or the oceans (marine microbiome)

    • includes also the entire collection of microbial genes present in any bacteria of these microbial communities

Introduction & Literature

The Human Microbiome

American Academy of Microbiology, 2013

How the microbiome shapes our world.

TED interview with Jonathan Eisen, Jessica Green, & Rob Knight

Microbiology: Metagenomics

by Philip Hugenholtz and Gene W. Tyson

Microbial Metagenomics: Beyond the Genome

by Jack A. Gilbert and Christopher L. Dupont

Staying Current in Bioinformatics & Genomics

How to find out the most recent trends in Genomics, by Stephen Turner

Microbiome Digest

recently published microbiology papers, selected by Elisabeth Bik


search for "microbiome", "microbiota" , "metagenomics"...

Help / discussions

biostars.org forum

Metagenomics sampling projects

→ Human Microbiome Project (HMP)

→ Earth Microbiome Project

→ Tara Oceans Expedition

Find more public available sampling datasets:




BLAST, Bowtie2, SAMtools, Assembly ...