Industrialization drives convergent microbiome and host physiological shifts in the human metaorganism

Poyet M 1 , Rühlemann M 2 , Schaan AP 3 , Ma Y 4 , Moitinho-Silva L 5 , Wacker EM 6 Show all authors , Jebens H 5 , Patel L 7 , Nguyen LTT 8 , Zimmer A 9 , Plichta D 10 , McDonald D 11 , Stevens C 10 , Agyei A 12 , Afihene MY 13 , Asibey SO 14 , Awuku YA 15 , Badiane AS 16 , Corzett C 17 , Deme A 18 , Dominguez-Rodrigo M 19 , Duah A 20 , Fezeu A 21 , Froment A 22 , Gibbons S 23 , Girard C 24 , Hooker J 25 , Ibrahim F 26 , Iqaluk D 27 , Juimo V 28 , Kettunen P 29 , Lafosse S 30 , Lango-Yaya E 31 , Lee SC 32 , Lehtimäki J 29 , Lim YAL 33 , Mabulla A 34 , Mahachai V 35 , Mohamed RS 36 , Moniz K 37 , Mwikarago IE 38 , Nartey YA 39 , Ndiaye D 16 , Noel M 25 , Onyekwere C 40 , Pin TM 26 , Plymoth A 39 , Roberts L 41 , Ruokolainen L 29 , Rusine J 42 , Segurel L 43 , Shapiro BJ 44 , Sigwazi S 45 , Sistiaga A 46 , Valles K 47 , Vatanen T 48 , Vilaichone RK 49 , Rosenstiel P 6 , Baines J 50 , Franke A 51 , Ellinghaus D 6 , Knight R 52 , Daly M 10 , Xavier RJ 53 , Alm EJ 54 , Groussin M 55

Affiliations 

  • 1 Institute of Experimental Medicine, Kiel University, Kiel, Germany; The Global Microbiome Conservancy (GMbC); Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Kiel Metaorganism Center, Kiel University, Kiel, Germany. Electronic address: m.poyet@iem.uni-kiel.de
  • 2 Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany; Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
  • 3 Institute of Experimental Medicine, Kiel University, Kiel, Germany; The Global Microbiome Conservancy (GMbC)
  • 4 Institute of Experimental Medicine, Kiel University, Kiel, Germany; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany; Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
  • 5 Institute of Experimental Medicine, Kiel University, Kiel, Germany; The Global Microbiome Conservancy (GMbC); Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
  • 6 Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
  • 7 Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Medical Scientist Training Program, University of California, San Diego, La Jolla, CA, USA
  • 8 The Global Microbiome Conservancy (GMbC); Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
  • 9 Unité de recherche en Architecture, University of Liege, Liège, Belgium
  • 10 The Broad Institute of MIT and Harvard, Cambridge, MA, USA
  • 11 Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
  • 12 The Global Microbiome Conservancy (GMbC); Department of Medicine and Therapeutics, University of Ghana Medical School and Korle Bu Teaching Hospital, Accra, Ghana
  • 13 The Global Microbiome Conservancy (GMbC); Department of Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
  • 14 The Global Microbiome Conservancy (GMbC); Catholic University College, Sunyani, Ghana
  • 15 The Global Microbiome Conservancy (GMbC); Department of Internal Medicine and Therapeutics, School of Medical Sciences, University of Cape Coast, Cape Coast, Ghana
  • 16 The Global Microbiome Conservancy (GMbC); Cheikh Anta Diop University, Dakar, Senegal
  • 17 The Global Microbiome Conservancy (GMbC); University of Southern California, CA, USA
  • 18 The Global Microbiome Conservancy (GMbC); Aristide Le Dantec Hospital, Dakar, Senegal
  • 19 Institute of Evolution in Africa (I.D.E.A.), Rice University and Archaeological and Paleontological Museum of Madrid, Spain; Department of Anthropology, Rice University, Houston, TX, USA
  • 20 The Global Microbiome Conservancy (GMbC); Department of Internal Medicine, University of Ghana Medical Centre, Legon, Accra, Ghana
  • 21 Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Institut de Recherche pour le Développement, Yaounde, Cameroon
  • 22 Institut de Recherche pour le Développement UMR 208, Muséum National d'Histoire Naturelle, Paris, France
  • 23 The Global Microbiome Conservancy (GMbC); Institute for Systems Biology, Seattle, USA; Department of Bioengineering, University of Washington, Seattle, USA; Department of Genome Sciences, University of Washington, Seattle, USA; eScience Institute, University of Washington, Seattle, USA
  • 24 The Global Microbiome Conservancy (GMbC); Université de Montréal, Département de sciences biologiques, C.P. 6128, succursale Centre-ville, Montréal, QC, Canada; Centre d'études nordiques, Département de Biochimie, de microbiologie et de bio-informatique, Université Laval, 1030 rue de la Médecine, Québec, QC, Canada
  • 25 The Global Microbiome Conservancy (GMbC); Chief Dull Knife College, Lame Deer, MT, USA
  • 26 The Global Microbiome Conservancy (GMbC); Center for Innovation in Medical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur, Malaysia; Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
  • 27 The Global Microbiome Conservancy (GMbC); Resolute Bay, Nunavut, NU, Canada
  • 28 The Global Microbiome Conservancy (GMbC); Institut de Recherche pour le Développement, Yaounde, Cameroon
  • 29 The Global Microbiome Conservancy (GMbC); Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
  • 30 The Global Microbiome Conservancy (GMbC); Institut de Recherche pour le Développement UMR 208, Muséum National d'Histoire Naturelle, Paris, France
  • 31 The Global Microbiome Conservancy (GMbC); University of Bangui, Bangui, Central African Republic
  • 32 The Global Microbiome Conservancy (GMbC); National Institute of Allergy and Infectious Diseases (NIAID), Rockville, MD, USA; Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
  • 33 The Global Microbiome Conservancy (GMbC); Center for Innovation in Medical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur, Malaysia; Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
  • 34 The Global Microbiome Conservancy (GMbC); Department of Archaeology and Heritage Studies, University of Dar es Salaam, Tanzania
  • 35 The Global Microbiome Conservancy (GMbC); Chulalongkorn University, Bangkok, Thailand
  • 36 The Global Microbiome Conservancy (GMbC); SAMRC Developmental Pathways for Health Research Unit, Faculty of Health Sciences University of the Witwatersrand, Johannesburg, South Africa
  • 37 Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
  • 38 The Global Microbiome Conservancy (GMbC); National Reference Laboratory, Kigali, Rwanda; Rwanda FDA and College of Medicine, Kigali, Rwanda; Health Science of the University of Rwanda, Kigali, Rwanda
  • 39 The Global Microbiome Conservancy (GMbC); Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
  • 40 The Global Microbiome Conservancy (GMbC); Department of Medicine, Lagos State University College of Medicine, Lagos, Nigeria
  • 41 The Global Microbiome Conservancy (GMbC); Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, USA
  • 42 The Global Microbiome Conservancy (GMbC); National Institute of Allergy and Infectious Diseases (NIAID), Rockville, MD, USA; National Reference Laboratory, Kigali, Rwanda
  • 43 Laboratoire de Biométrie et Biologie Evolutive UMR5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
  • 44 The Global Microbiome Conservancy (GMbC); Department of Microbiology and Immunology, McGill University Montreal, Canada / McGill Genome Centre, McGill University, Montreal, Montreal, QC, Canada
  • 45 The Global Microbiome Conservancy (GMbC); Tumaini University Makumira, Arusha, Tanzania
  • 46 The Global Microbiome Conservancy (GMbC); Globe Institute, University of Copenhagen, Copenhagen, Denmark; Geosciences Department, Aarhus University, Aarhus, Denmark
  • 47 The Global Microbiome Conservancy (GMbC); Medical Scientist Training Program, Mayo Clinic, Rochester, USA
  • 48 The Global Microbiome Conservancy (GMbC); The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Liggins Institute, University of Auckland, Auckland, New Zealand
  • 49 The Global Microbiome Conservancy (GMbC); Thammasat University Hospital, Bangkok, Thailand
  • 50 Institute of Experimental Medicine, Kiel University, Kiel, Germany; Kiel Metaorganism Center, Kiel University, Kiel, Germany; Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
  • 51 Kiel Metaorganism Center, Kiel University, Kiel, Germany; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
  • 52 Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; UCSD Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, CA, USA
  • 53 The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
  • 54 The Global Microbiome Conservancy (GMbC); Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA. Electronic address: ejalm@mit.edu
  • 55 The Global Microbiome Conservancy (GMbC); Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Kiel Metaorganism Center, Kiel University, Kiel, Germany; Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany. Electronic address: m.groussin@ikmb.uni-kiel.de
Cell, 2026 Nov 02.
PMID: 42971202 DOI: 10.1016/j.cell.2026.10.016

Abstract

Understanding how industrialization reshapes the human metaorganism requires integrating microbiome ecology with host physiology across globally diverse populations. Here, we generate multivariate data from the Global Microbiome Conservancy cohort, including gut microbiome, immunoglobulin A (IgA) sequencing, host genotyping, diet, lifestyle, and fecal biomarker profiles, to investigate host-microbiome interactions across gradients of industrialization and geography. We show that industrialization is associated with homogenized microbial compositions, reduced microbial diversity, and lower community stability, independent of host confounders. We further show that industrialization is linked to elevated markers of gut stress, increased IgA secretion, and altered patterns of IgA-bacteria interactions. Finally, we show that microbiome-based disease predictors trained on industrialized populations are uninformative in less industrialized cohorts, highlighting limited cross-population transferability. Together, our results reveal coordinated restructuring of the microbial ecosystem and host physiology and emphasize the need for inclusive, globally representative data to improve translational microbiome applications across diverse human populations.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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