A microbiome is the community of microorganisms that can usually be found living together in any given habitat. Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples.

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.


Before diving into this topic, we recommend you to have a look at:

Not sure where to start?

Try the Microbiome Learning Pathway! Start Learning



Start here if you are new to microbiome analyses in Galaxy.

Lesson Slides Hands-on Recordings Input dataset Workflows
Analyses of metagenomics data - The global picture

Metabarcoding / Amplicon analyses

Taxonomic characterisation of mixed samples using a single gene region.

Lesson Slides Hands-on Recordings Input dataset Workflows
16S Microbial analysis with Nanopore data
Antibiotic resistance detection
QIIME 2 Cancer Microbiome Intervention external-link
QIIME 2 Moving Pictures external-link
16S Microbial Analysis with mothur (extended)
16S Microbial Analysis with mothur (short)


Taxonomic and functional characterisation and assembly of mixed samples using whole genome data.

Lesson Slides Hands-on Recordings Input dataset Workflows
Assembly of metagenomic sequencing data
Binning of metagenomic sequencing data
Identification of the micro-organisms in a beer using Nanopore sequencing
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
Taxonomic Profiling and Visualization of Metagenomic Data


Taxonomic and functional characterisation of mixed samples using transcriptome data.

Lesson Slides Hands-on Recordings Input dataset Workflows
Metatranscriptomics analysis using microbiome RNA-seq data
Metatranscriptomics analysis using microbiome RNA-seq data (short)


Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Microbiome Analysis

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80 quay.io/galaxy/metagenomics-training

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoBérénice Batut avatar Bérénice Batutorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoPaul Zierep avatar Paul Zierep

For any question related to this topic and the content, you can contact them or visit our Gitter channel.


This material was contributed to by:

Praveen Kumar avatar Praveen KumarSophia Hampe avatar Sophia HampeQIIME2 avatar QIIME2Emma Leith avatar Emma LeithWillem de Koning avatar Willem de Koningorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoDave Clements avatar Dave Clementsorcid logoFotis E. Psomopoulos avatar Fotis E. Psomopoulosorcid logoSubina Mehta avatar Subina Mehtaorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoSaskia Hiltemann avatar Saskia HiltemannTeresa Müller avatar Teresa Müllerorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoBérénice Batut avatar Bérénice BatutSiyu Chen avatar Siyu ChenRay Sajulga avatar Ray Sajulgaorcid logoPaul Zierep avatar Paul Ziereporcid logoEngy Nasr avatar Engy Nasrorcid logoNikolaos Pechlivanis avatar Nikolaos Pechlivanisorcid logoPolina Polunina avatar Polina Polunina


This material was funded by:

EOSC-Life avatar EOSC-LifeGallantries: Bridging Training Communities in Life Science, Environment and Health avatar Gallantries