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
Detection of shared microbial strains with SameStr
metagenomics microbiome microgalaxy
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
Remove contamination and host reads
host-removal preprocessing metagenomics microgalaxy
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

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

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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 logoSantino Faack avatar Santino Faackorcid logoVini Salazar avatar Vini Salazarorcid logoTeresa Müller avatar Teresa Müllerorcid logoBérénice Batut avatar Bérénice Batutorcid logoXenia Morera Martínez avatar Xenia Morera MartínezIgor Makunin avatar Igor Makuninorcid logoPratik Jagtap avatar Pratik JagtapSiyu Chen avatar Siyu ChenBethan Manley avatar Bethan Manleyorcid logoFabio Cumbo avatar Fabio CumboRay Sajulga avatar Ray SajulgaNuwan Goonasekera avatar Nuwan GoonasekeraDidier Debroas avatar Didier Debroasorcid logoMina Hojat Ansari avatar Mina Hojat Ansariorcid logoClea Siguret avatar Clea Siguretorcid logoEngy Nasr avatar Engy Nasrorcid logoRand Zoabi avatar Rand ZoabiWillem de Koning avatar Willem de Koningorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoHans-Rudolf Hotz avatar Hans-Rudolf HotzEmma Leith avatar Emma Leithorcid logoFotis E. Psomopoulos avatar Fotis E. PsomopoulosNiall Beard avatar Niall BeardTarnima Omara avatar Tarnima Omaraorcid logoLinelle Abueg avatar Linelle AbuegKatherine Do avatar Katherine DoSophia Hampe avatar Sophia Hampeorcid logoArmin Dadras avatar Armin Dadrasorcid logoSubina Mehta avatar Subina Mehtaorcid logoPaul Zierep avatar Paul ZierepNatalie Whitaker-Allen avatar Natalie Whitaker-Allenorcid logoPolina Polunina avatar Polina Poluninaorcid logoBjörn Grüning avatar Björn Grüningorcid logoTimothy J. Griffin avatar Timothy J. GriffinWilliam Durand avatar William DurandDechen Bhuming avatar Dechen BhumingSujai Kumar avatar Sujai KumarPraveen Kumar avatar Praveen Kumarorcid logoNikos Pechlivanis avatar Nikos Pechlivanisorcid logoAnna Syme avatar Anna SymeMichael Thang avatar Michael Thangorcid logoMatthias Bernt avatar Matthias Berntorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoNadia Goué avatar Nadia GouéChristine Oger avatar Christine Ogerorcid logoBert Droesbeke avatar Bert Droesbekeorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoGiuseppe Defazio avatar Giuseppe Defazioorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoHelena Rasche avatar Helena Rascheorcid logoDave Clements avatar Dave Clementsorcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoSaskia Hiltemann avatar Saskia Hiltemann

Funding

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

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The University of Melbourne
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de.KCD
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ELIXIR Europe
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IFB
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Australian BioCommons
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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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EOSC-Life
EOSC-Life has received funding from the European Union’s Horizon 2020 programme under grant agreement number 824087
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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