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 () and tutorial () buttons below.

Introduction

Start here if you are new to microbiome analyses in Galaxy.

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to Microbiome Analysis
Analyses of metagenomics data - The global picture
microgalaxy

Metabarcoding / Amplicon analyses

Taxonomic characterisation of mixed samples using a single gene region.

Lesson Slides Hands-on Recordings Input dataset Workflows
16S Microbial analysis with Nanopore data
metabarcoding 16S nanopore microgalaxy plants
Antibiotic resistance detection
nanopore plasmids assembly amr microgalaxy
Building an amplicon sequence variant (ASV) table from 16S data using DADA2
metabarcoding 16S microgalaxy
MGnify v5.0 Amplicon Pipeline
microbiome amplicon taxonomy taxonomic abundance
QIIME 2 Cancer Microbiome Intervention
metabarcoding 16S taxonomic profiling diversity microgalaxy
QIIME 2 Moving Pictures
metagenomics taxonomic profiling diversity microgalaxy
16S Microbial Analysis with mothur (extended)
metabarcoding 16S microgalaxy
16S Microbial Analysis with mothur (short)
metabarcoding 16S microgalaxy

Metagenomics

Taxonomic and functional characterisation and assembly of mixed samples using whole genome data.

Lesson Slides Hands-on Recordings Input dataset Workflows
Assembly of metagenomic sequencing data
assembly metagenomics microgalaxy
Binning of metagenomic sequencing data
binning metagenomics microgalaxy
Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads
assembly binning metagenomics microgalaxy
Calculating α and β diversity from microbiome taxonomic data
metagenomics diversity
Identification of the micro-organisms in a beer using Nanopore sequencing
nanopore beer citizen science metagenomics microgalaxy
Indexing and profiling microbes with MetaSBT
metagenomics diversity taxonomic profiling
Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
microgalaxy Nanopore data analysis Pathogens detection Phylogenetic tree Heatmap cyoa
Taxonomic Profiling and Visualization of Metagenomic Data
metagenomics taxonomic profiling microgalaxy

Metatranscriptomics

Taxonomic and functional characterisation of mixed samples using transcriptome data.

Lesson Slides Hands-on Recordings Input dataset Workflows
Metatranscriptomics analysis using microbiome RNA-seq data
metatranscriptomics microgalaxy
Metatranscriptomics analysis using microbiome RNA-seq data (short)
metatranscriptomics microgalaxy

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
Clinical Metaproteomics 1: Database-Generation
label-TMT11
Clinical Metaproteomics 2: Discovery
label-TMT11
Clinical Metaproteomics 3: Verification
label-TMT11
Clinical Metaproteomics 4: Quantitation
label-TMT11
Clinical Metaproteomics 5: Data Interpretation
label-TMT11

Other

Assorted Tutorials

Lesson Slides Hands-on Recordings Input dataset Workflows
Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2
fungi ecology
Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data
Remove contamination and host reads

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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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoBérénice Batut avatar Bérénice Batutorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoPaul Zierep avatar Paul Zierep

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Contributors

This material was contributed to by:

orcid logoTeresa Müller avatar Teresa Müllerorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoSaskia Hiltemann avatar Saskia HiltemannSophia Hampe avatar Sophia HampeIgor Makunin avatar Igor MakuninWillem de Koning avatar Willem de Koningorcid logoClea Siguret avatar Clea Siguretorcid logoPaul Zierep avatar Paul Ziereporcid logoTimothy J. Griffin avatar Timothy J. GriffinBethan Manley avatar Bethan Manleyorcid logoEngy Nasr avatar Engy NasrSiyu Chen avatar Siyu Chenorcid logoDeepti Varshney avatar Deepti VarshneyNuwan Goonasekera avatar Nuwan Goonasekeraorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosPraveen Kumar avatar Praveen Kumarorcid logoMina Hojat Ansari avatar Mina Hojat Ansariorcid logoDave Clements avatar Dave Clementsorcid logoPratik Jagtap avatar Pratik JagtapMatthias Bernt avatar Matthias Berntorcid logoNicola Soranzo avatar Nicola SoranzoDidier Debroas avatar Didier Debroasorcid logoWolfgang Maier avatar Wolfgang MaierRay Sajulga avatar Ray Sajulgaorcid logoNikos Pechlivanis avatar Nikos Pechlivanisorcid logoBjörn Grüning avatar Björn GrüningTarnima Omara avatar Tarnima Omaraorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoNadia Goué avatar Nadia GouéEmma Leith avatar Emma Leithorcid logoVini Salazar avatar Vini Salazarorcid logoDaniel Blankenberg avatar Daniel BlankenbergChristine Oger avatar Christine Ogerorcid logoAnna Syme avatar Anna SymeSujai Kumar avatar Sujai KumarNiall Beard avatar Niall Beardorcid logoHans-Rudolf Hotz avatar Hans-Rudolf Hotzorcid logoBérénice Batut avatar Bérénice BatutWilliam Durand avatar William DurandMichael Thang avatar Michael ThangKatherine Do avatar Katherine Doorcid logoRand Zoabi avatar Rand Zoabiorcid logoPolina Polunina avatar Polina Poluninaorcid logoHelena Rasche avatar Helena Rascheorcid logoLinelle Abueg avatar Linelle AbuegDechen Bhuming avatar Dechen Bhumingorcid logoFabio Cumbo avatar Fabio CumboSantino Faack avatar Santino Faackorcid logoSubina Mehta avatar Subina Mehtaorcid logoCristóbal Gallardo avatar Cristóbal Gallardo

Funding

These individuals or organisations provided funding support for the development of this resource

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ELIXIR Europe
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Melbourne Bioinformatics
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SPUN
SPUN is a scientific research organization founded to map mycorrhizal fungal communities and advocate for their protection.
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de.KCD
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Australian BioCommons
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The University of Melbourne
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EOSC-Life
EOSC-Life has received funding from the European Union’s Horizon 2020 programme under grant agreement number 824087
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IFB
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Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.

References