Integrating multi-omics technologies to decipher microbiome functions
Nature Communications, vol. 17
Abstract
Multi-omics approaches have revolutionized our understanding of microbial communities by enabling simultaneous interrogation of genomic, transcriptomic, proteomic, and metabolomic data. The systematic integration and analysis of these deep datasets help decipher the functional roles of microbiomes, providing critical insights into microbial activities, interactions, and dynamics across diverse environments. Biological complexity makes multi-omics analysis of a single, isolated organism demanding but highly informative, yet this complexity increases further when samples comprise hundreds to thousands of individual species. As microbiome research continues to expand into clinical, environmental, and engineered systems, standardized workflows, benchmarked datasets, and community-driven initiatives are essential to ensure reproducibility, standardization and interpretability. Establishing and disseminating best practices for experimental design, data processing, and integrative analyses will be critical for maximizing comparability and scientific rigor across studies. This perspective highlights recent advances in multi-omics microbiome research, outlines key obstacles in data integration and metadata harmonization, and proposes a collaborative roadmap for scalable, FAIR-compliant multi-omics investigations and potentially disruptive Artificial Intelligence (AI) advances comparable to those of AlphaFold in the field of microbiome science.
Authors 45
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Ghent University · VIB-UGent Center for Medical Biotechnology
Affiliation as printed
CompOmics, VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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Georgia Institute of Technology
Affiliation as printed
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
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Norwegian University of Life Sciences
Affiliation as printed
Faculty of Biosciences, Norwegian, University of Life Sciences, Ås, Norway
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North Carolina State University
Affiliation as printed
Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
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Affiliation as printed
Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, Bielefeld, Germany
Multidimensional Omics Analyses group, Faculty of Technology, Bielefeld University, Bielefeld, Germany
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Luxembourg Institute of Health
Affiliation as printed
Bioinformatics and Artificial Intelligence, Department of Medical Informatics, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
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Affiliation as printed
Department of Biochemistry and Molecular Biology, Infection Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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Max Planck Institute for Dynamics of Complex Technical Systems · Otto-von-Guericke-Universität Magdeburg
Affiliation as printed
Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, Magdeburg, Germany
Otto-von-Guericke-University Magdeburg, Bioprocess Engineering, Universitätsplatz 2, Magdeburg, Germany
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Ghent University · VIB-UGent Center for Medical Biotechnology
Affiliation as printed
CompOmics, VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
Department of Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
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Affiliation as printed
Department of Biochemistry, Molecular Biology and Biophysics, 321 University of Minnesota, 6-155 Jackson Hall, 321 Church Street SE, University of Minnesota, Minneapolis, MN, USA
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Leiden University · Leiden University Medical Center
Affiliation as printed
Center for Microbiome Analyses and Therapeutics, Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, ZA, the Netherlands
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Åbo Akademi University · University of Turku
Affiliation as printed
Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
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Affiliation as printed
Systems Biology of Pain, Division of Pharmacology & Toxicology, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, Vienna, Austria
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National Institute of Oceanography
Affiliation as printed
Biological Oceanography Division, CSIR- National Institute of Oceanography, Dona Paula, Goa, India
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Centre National de la Recherche Scientifique · Institut Pluridisciplinaire Hubert Curien · Ghent University · VIB-UGent Center for Medical Biotechnology · Université de Strasbourg
Affiliation as printed
BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC UMR7178, CNRS, Université de Strasbourg, Strasbourg, France
CompOmics, VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
Infrastructure Nationale de Protéomique ProFI-UAR, Strasbourg, France
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Anhalt University of Applied Sciences · Max Planck Institute for Dynamics of Complex Technical Systems · Otto-von-Guericke-Universität Magdeburg
Affiliation as printed
Applied Biosciences and Process Engineering, Anhalt University of Applied Sciences, Bernburger Str. 55, Köthen, Germany
Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, Magdeburg, Germany
Otto-von-Guericke-University Magdeburg, Bioprocess Engineering, Universitätsplatz 2, Magdeburg, Germany
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National Institute of Oceanography
Affiliation as printed
Biological Oceanography Division, CSIR- National Institute of Oceanography, Dona Paula, Goa, India
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Amsterdam University Medical Centers
Affiliation as printed
Center for Infection and Molecular Medicine, Amsterdam UMC, Amsterdam, The Netherlands
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Helmholtz Centre for Environmental Research
Affiliation as printed
Department of Molecular Toxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, Leipzig, Germany
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Pacific Northwest National Laboratory · Environmental Molecular Sciences Laboratory
Affiliation as printed
Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands
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University of East Anglia · Norwich Research Park · Quadram Institute
Affiliation as printed
Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK, University of East Anglia, Norwich, Norfolk, UK
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Affiliation as printed
Department of Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
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Leiden University Medical Center
Affiliation as printed
Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, RC, The Netherlands
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Affiliation as printed
Biosciences Division, Oak RIdge National Laboratory, Oak Ridge, TN, USA
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Åbo Akademi University · University of Turku
Affiliation as printed
Institute of Biomedicine, University of Turku, Turku, Finland
Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
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European Bioinformatics Institute
Affiliation as printed
European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
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Georgia Institute of Technology
Affiliation as printed
School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
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Lawrence Berkeley National Laboratory · University of California, Merced · Joint Genome Institute
Affiliation as printed
Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA
School of Natural Sciences, University of California at Merced, 5200 Lake Rd, Merced, CA, USA
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Affiliation as printed
Biotechnology Division, Department of Biology, Faculty of Science, Istanbul University, Istanbul, Türkiye
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Pacific Northwest National Laboratory
Affiliation as printed
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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Affiliation as printed
Department of Biochemistry, Molecular Biology and Biophysics, 321 University of Minnesota, 6-155 Jackson Hall, 321 Church Street SE, University of Minnesota, Minneapolis, MN, USA
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Affiliation as printed
Laboratory of Hepato-Gastroenterology, Institute of Experimental and Clinical Research, UCLouvain, Brussels, Belgium
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Bielefeld University · Leibniz Institute for Analytical Sciences - ISAS
Affiliation as printed
Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
Multidimensional Omics Analyses group, Faculty of Technology, Bielefeld University, Bielefeld, Germany
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands
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Université de Technologie de Compiègne · Centre National de la Recherche Scientifique · Biofonderie de l'Alliance Sorbonne Université
Affiliation as printed
Biofonderie de l'Alliance Sorbonne Université, UAR 2037, Sorbonne Université, CNRS, Université de Technologie de Compiègne, 75005, Paris, Cedex, France
International Research Hub for Marine Pollutions CIC, Technology House, Glasgow, UK
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Affiliation as printed
Center of Excellence for Metaproteomics University of Vienna - Bruker Daltonics, University of Vienna, Vienna, Austria
Systems Biology of Pain, Division of Pharmacology & Toxicology, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, Vienna, Austria
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Affiliation as printed
Data Competence Center MF 2, Robert Koch Institute, Berlin, Germany
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Affiliation as printed
Frazer Institute, The University of Queensland, Woolloongabba, Brisbane, Queensland, Australia
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Commissariat à l'Énergie Atomique et aux Énergies Alternatives · Université Paris-Saclay · Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement · Médicaments et Technologies pour la Santé · Proteomics French Infrastructure Core
Affiliation as printed
Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, Bagnols-sur-Cèze, France
Infrastructure Nationale de Protéomique, ProFI, UAR 2048, Bagnols-sur-Cèze, France
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European Bioinformatics Institute
Affiliation as printed
European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
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University of Luxembourg · Luxembourg Centre for Systems Biomedicine
Affiliation as printed
Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg and Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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Affiliation as printed
Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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Commissariat à l'Énergie Atomique et aux Énergies Alternatives · Université Paris-Saclay · Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement · Médicaments et Technologies pour la Santé · Proteomics French Infrastructure Core
Affiliation as printed
Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, Bagnols-sur-Cèze, France
Infrastructure Nationale de Protéomique, ProFI, UAR 2048, Bagnols-sur-Cèze, France
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Pratik Dilip Jagtap corresponding
Affiliation as printed
Department of Biochemistry, Molecular Biology and Biophysics, 321 University of Minnesota, 6-155 Jackson Hall, 321 Church Street SE, University of Minnesota, Minneapolis, MN, USA. pjagtap@umn.edu
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