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