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