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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Learning Pathways
Or have a look at one of our learning pathways involving this topic. Learning pathways are sets of tutorials curated for you by community experts to form a coherent set of lessons around a topic, building up knowledge as you go. We always recommend to follow the tutorials in the order they are listed in the pathway.
Frequently Asked Questions
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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:
Hans-Rudolf Hotz
Gayle Philip
Sujai Kumar
Fabio Cumbo
Linelle Abueg
Niall Beard
Xenia Morera Martínez
Sophia Hampe
Daniel Blankenberg
Tristan Reynolds
Michael Thang
Natalie Whitaker-Allen
Laura Geissler
Santino Faack
Engy Nasr
Nikos Pechlivanis
Matthias Bernt
Subina Mehta
Paul Zierep
Praveen Kumar
Bérénice Batut
Teresa Müller
Clea Siguret
Nuwan Goonasekera
Ray Sajulga
Katherine Do
Willem de Koning
Björn Grüning
Nadia Goué
Ashley Dungan
Helena Rasche
Anna Syme
Saskia Hiltemann
Fotis E. Psomopoulos
Cristóbal Gallardo
Vini Salazar
Christine Oger
Bert Droesbeke
William Durand
Polina Polunina
Dave Clements
Wolfgang Maier
Igor Makunin
Siyu Chen
Dechen Bhuming
Mina Hojat Ansari
Pratik Jagtap
Nicola Soranzo
Rand Zoabi
Armin Dadras
Deepti Varshney
Timothy J. Griffin
Bethan Manley
Emma Leith
Tarnima Omara
Emma Gail
Didier Debroas
Giuseppe Defazio
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.