Microbiology Galaxy Lab: a community-driven gateway for reproducible and FAIR analysis of microbiological data

The explosion of microbial omics data has outpaced the ability of many researchers to analyse it, with complex tools and limited computational resources creating barriers to discovery. To address this gap, we present the Microbiology Galaxy Lab (MGL): a free, globally accessible, community-supported platform that combines state-of-the-art analytical power with user-friendly accessibility. Supported by the Galaxy and global microbiology communities, this platform integrates over 315 tool suites and 115 curated workflows, enabling comprehensive metabarcoding, (meta)genomic, (meta)transcriptomic, and (meta)proteomic data analysis within a FAIR-aligned environment. It also supports research in the health and infectious disease sectors, as well as in environmental microbiology. The platform's utility is exemplified through various use cases, including antimicrobial resistance tracking, biomarker prediction, microbiome classification, and functional annotation of key microbes. Built on reproducibility and community engagement, it supports the creation, sharing, and updating of best-practice workflows. Over 35 tutorials and learning paths empower scientists, fostering an ecosystem that keeps resources at the forefront of microbiological data analysis. The MGL enables collective analysis, democratising research, thereby accelerating discovery across the global microbiology community ( microbiology.usegalaxy.org , .eu , .org.au , . fr ).

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Journal
Communications Biology
Published
2026-10-29
DOI
https://doi.org/10.1038/s42003-026-10750-7
Primary Topic
Scientific Computing and Data Management
Type
article
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article

Microbiology Galaxy Lab: a community-driven gateway for reproducible and FAIR analysis of microbiological data

Muneer Ahmad Malla, Björn Andreas Grüning, Gareth R. Price, Tiffanie Maree Nelson et al.
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Communications Biology
Scientific Computing and Data Management
article

Microbiology Galaxy Lab: a community-driven gateway for reproducible and FAIR analysis of microbiological data

Muneer Ahmad Malla, Björn Andreas Grüning, Gareth R. Price, Tiffanie Maree Nelson, Nikolaos Pechlivanis, Fabio Cumbo, Kimberly L. Kanapeckas Métris, Raphaëlle Péguilhan, Saskia Hiltemann, Bérénice Batut, Timothy J. Griffin, Asime Oba, Cameron J. Hyde, Nicola Soranzo, Matthias Bernt, Daniela Brites, Anshu Bhardwaj, Paul F. Zierep, Engy Mohamed Taha Nasr, Michael C. Schatz, Mustafa Vohra, Pratik Dilip Jagtap, Nikolaos Strepis, Emanuele Ferrari, Daniel J Blankenberg, Fotis E Psomopoulos, Cléa Siguret, Subina Mehta, Pierre Amato, Christina Pavloudi, Nedeljka N. Rosic, Valerie C. Schiml, Peter Van Heusden, Andrew Stubbs, Saim Momin, Ashwani Kumar, Katherine T. Do
article en

Abstract

The explosion of microbial omics data has outpaced the ability of many researchers to analyse it, with complex tools and limited computational resources creating barriers to discovery. To address this gap, we present the Microbiology Galaxy Lab (MGL): a free, globally accessible, community-supported platform that combines state-of-the-art analytical power with user-friendly accessibility. Supported by the Galaxy and global microbiology communities, this platform integrates over 315 tool suites and 115 curated workflows, enabling comprehensive metabarcoding, (meta)genomic, (meta)transcriptomic, and (meta)proteomic data analysis within a FAIR-aligned environment. It also supports research in the health and infectious disease sectors, as well as in environmental microbiology. The platform's utility is exemplified through various use cases, including antimicrobial resistance tracking, biomarker prediction, microbiome classification, and functional annotation of key microbes. Built on reproducibility and community engagement, it supports the creation, sharing, and updating of best-practice workflows. Over 35 tutorials and learning paths empower scientists, fostering an ecosystem that keeps resources at the forefront of microbiological data analysis. The MGL enables collective analysis, democratising research, thereby accelerating discovery across the global microbiology community ( microbiology.usegalaxy.org , .eu , .org.au , . fr ).

Communications BiologyVol. 9(1)
Lovely Professional University (IN), Centre National de la Recherche Scientifique (FR), University of Minnesota (US), Cleveland Clinic (US), Helmholtz Centre for Environmental Research (DE), Johns Hopkins University (US), Inserm (FR), Swiss Tropical and Public Health Institute (CH), University of Freiburg (DE), The University of Queensland (AU), The University of Melbourne (AU), University of Allahabad (IN), University of Basel (CH), Université Clermont Auvergne (FR), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR), German Centre for Integrative Biodiversity Research (DE), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), Earlham Institute (GB), Water Research Institute (IT), Laboratoire Microorganismes Génome et Environnement (FR), Centre for Research and Technology Hellas (GR), Institut Français de Bioinformatique (FR), Institute of Microbial Technology (IN), Erasmus MC Cancer Institute (NL), National Research Council (IT), QCIF Ltd. (AU), European Marine Biological Resource Centre (FR), NAMO Medical Education & Research Institute (IN), Cleveland Clinic Research (US), Norwegian University of Life Sciences (NO), University of Maiduguri (NG), Council of Scientific and Industrial Research (IN), Southern Cross University (AU), Clemson University (US), University of the Western Cape (ZA), Technical University of Denmark (DK)
Bill and Melinda Gates Foundation, Alexander von Humboldt-Stiftung, Clemson University, University of Minnesota, Cleveland Clinic, Johns Hopkins University, Universität Basel, Wellcome Trust, Institut Français de Bioinformatique, European Commission, Agence Nationale de la Recherche, Institut National de la Santé et de la Recherche Médicale, Southern Cross University, University of Melbourne, University of Queensland, Bundesministerium für Bildung und Forschung, Albert-Ludwigs-Universität Freiburg, University of the Western Cape, Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg, Centre National de la Recherche Scientifique, Helmholtz-Zentrum für Umweltforschung, Danmarks Tekniske Universitet, Norges Miljø- og Biovitenskapelige Universitet, German Network for Bioinformatics Infrastructure, Lovely Professional University, Deutsches Zentrum für integrative Biodiversitätsforschung Halle-Jena-Leipzig, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, National Institutes of Health, HORIZON EUROPE Framework Programme, CSIR - Institute of Microbial Technology
Openalex Percentile: Top 7%
Scientific Computing and Data Management
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