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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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:
Armin Dadras
Clea Siguret
Niall Beard
Praveen Kumar
Emma Leith
Hans-Rudolf Hotz
Tristan Reynolds
Katherine Do
Didier Debroas
Sophia Hampe
Willem de Koning
Santino Faack
Fotis E. Psomopoulos
Mina Hojat Ansari
Linelle Abueg
Pratik Jagtap
Fabio Cumbo
Nuwan Goonasekera
Giuseppe Defazio
Bérénice Batut
Nikos Pechlivanis
Vini Salazar
Tarnima Omara
Wolfgang Maier
Ray Sajulga
Dechen Bhuming
Björn Grüning
Nicola Soranzo
Matthias Bernt
Deepti Varshney
Natalie Whitaker-Allen
Helena Rasche
Subina Mehta
Teresa Müller
Igor Makunin
Michael Thang
Rand Zoabi
Cristóbal Gallardo
Timothy J. Griffin
Engy Nasr
Christine Oger
William Durand
Siyu Chen
Paul Zierep
Nadia Goué
Saskia Hiltemann
Daniel Blankenberg
Bert Droesbeke
Polina Polunina
Sujai Kumar
Dave Clements
Anna Syme
Bethan Manley
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.