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:
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Material
You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.Introduction
Start here if you are new to microbiome analyses in Galaxy.
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
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Introduction to Microbiome Analysis
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| Analyses of metagenomics data - The global picture |
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.
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
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| Metatranscriptomics analysis using microbiome RNA-seq data | |||||
| Metatranscriptomics analysis using microbiome RNA-seq data (short) |
Metaproteomics
These tutorials are step by step analysis from database generation to the discovery of peptides to verification, quantitation, and interpretation of the results.
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
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| Clinical Metaproteomics 1: Database-Generation | |||||
| Clinical Metaproteomics 2: Discovery | |||||
| Clinical Metaproteomics 3: Verification | |||||
| Clinical Metaproteomics 4: Quantitation | |||||
| Clinical Metaproteomics 5: Data Interpretation |
Other
Assorted Tutorials
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
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| Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2 | |||||
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Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data
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Remove contamination and host reads
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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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Community Resources
Community Home Maintainer HomeEditorial Board
This material is reviewed by our Editorial Board:
Bérénice Batut
Saskia Hiltemann
Paul Zierep
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Contributors
This material was contributed to by:
Emma Leith
Cristóbal Gallardo
Sophia Hampe
Saskia Hiltemann
Didier Debroas
Fabio Cumbo
Teresa Müller
Siyu Chen
Bérénice Batut
Katherine Do
Matthias Bernt
Helena Rasche
William Durand
Santino Faack
Niall Beard
Nuwan Goonasekera
Bert Droesbeke
Nadia Goué
Praveen Kumar
Anna Syme
Timothy J. Griffin
Engy Nasr
Nicola Soranzo
Tarnima Omara
Deepti Varshney
Daniel Blankenberg
Fotis E. Psomopoulos
Michael Thang
Wolfgang Maier
Tristan Reynolds
Vini Salazar
Björn Grüning
Subina Mehta
Nikos Pechlivanis
Polina Polunina
Paul Zierep
Sujai Kumar
Pratik Jagtap
Ray Sajulga
Dave Clements
Igor Makunin
Mina Hojat Ansari
Bethan Manley
Linelle Abueg
Willem de Koning
Dechen Bhuming
Clea Siguret
Hans-Rudolf Hotz
Christine Oger
Rand Zoabi
Funding
These individuals or organisations provided funding support for the development of this resource
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.