Microbiome

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.

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Requirements

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

• Introduction to Galaxy Analyses

Material

Introduction

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

Metabarcoding / Amplicon analyses

Taxonomic characterisation of mixed samples using a single gene region.

Metagenomics

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

Metatranscriptomics

Taxonomic and functional characterisation of mixed samples using transcriptome data.

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:

Bérénice Batut

Saskia Hiltemann

Paul Zierep

Contributors

This material was contributed to by:

Paul Zierep

Engy Nasr

Clea Siguret

Matthias Bernt

Fotis E. Psomopoulos

Cristóbal Gallardo

QIIME2

Siyu Chen

Bérénice Batut

Nikos Pechlivanis

Willem de Koning

Teresa Müller

Hans-Rudolf Hotz

Dave Clements

Polina Polunina

Ray Sajulga

Sophia Hampe

Praveen Kumar

Wolfgang Maier

Subina Mehta

Saskia Hiltemann

Pratik Jagtap

Emma Leith

Funding

These individuals or organisations provided funding support for the development of this resource

EOSC-Life

EOSC-Life has received funding from the European Union’s Horizon 2020 programme under grant agreement number 824087

Gallantries

This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.

References

• Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD.: Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology
• Pablo Yarza, Pelin Yilmaz, Elmar Pruesse, Frank Oliver Glöckner, Wolfgang Ludwig, Karl-Heinz Schleifer, William B. Whitman, Jean Euzéby, Rudolf Amann, Ramon Rosselló-Móra: Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences.