Convergent genomic evolution of human gut bacteria along an industrialization gradient

Rühlemann M 1 , Ma Y 2 , Szánthó LL 3 , Waschina S 4 , Moitinho-Silva L 5 , Mews LC 6 Show all authors , Faus-Camarena J 7 , Jebens H 5 , Costa J 5 , Juimo V 8 , Fezeu A 9 , Agyei A 10 , Afihene MY 11 , Asibey SO 12 , Awuku YA 13 , Duah A 14 , Nartey YA 15 , Ibrahim F 16 , Lim YAL 17 , Tan MP 17 , Onyekwere C 18 , Rusine J 19 , Mwikarago IE 20 , Baines J 21 , Franke A 22 , Szöllősi GJ 23 , Xavier RJ 24 , Alm EJ 25 , Groussin M 26 , Poyet M 27

Affiliations 

  • 1 The Global Microbiome Conservancy (GMbC); Institute of Clinical Molecular Biology, Kiel University & University Hospital Schleswig-Holstein, Kiel, Germany; Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
  • 2 Institute of Clinical Molecular Biology, Kiel University & University Hospital Schleswig-Holstein, Kiel, Germany; Institute of Experimental Medicine, Kiel University and University Schleswig-Holstein, Kiel, Germany; Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
  • 3 Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
  • 4 Division of Food Technology, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
  • 5 The Global Microbiome Conservancy (GMbC); Institute of Clinical Molecular Biology, Kiel University & University Hospital Schleswig-Holstein, Kiel, Germany; Institute of Experimental Medicine, Kiel University and University Schleswig-Holstein, Kiel, Germany
  • 6 Institute of Clinical Molecular Biology, Kiel University & University Hospital Schleswig-Holstein, Kiel, Germany; Institute of Experimental Medicine, Kiel University and University Schleswig-Holstein, Kiel, Germany
  • 7 Institute of Clinical Molecular Biology, Kiel University & University Hospital Schleswig-Holstein, Kiel, Germany
  • 8 The Global Microbiome Conservancy (GMbC); Division of Food Technology, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
  • 9 The Global Microbiome Conservancy (GMbC); Institut de Recherche pour le Développement, Yaounde, Cameroon
  • 10 The Global Microbiome Conservancy (GMbC); Department of Medicine and Therapeutics, University of Ghana Medical School and Korle Bu Teaching Hospital, Accra, Ghana
  • 11 The Global Microbiome Conservancy (GMbC); Department of Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
  • 12 The Global Microbiome Conservancy (GMbC); Catholic University College, Sunyani, Ghana
  • 13 The Global Microbiome Conservancy (GMbC); Department of Internal Medicine and Therapeutics, School of Medical Sciences University of Cape Coast, Cape Coast, Ghana
  • 14 The Global Microbiome Conservancy (GMbC); Department of Internal Medicine, University of Ghana Medical Centre, Legon, Accra, Ghana
  • 15 The Global Microbiome Conservancy (GMbC); Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
  • 16 The Global Microbiome Conservancy (GMbC); Centre for Innovation in Medical Engineering, University of Malaya, Kuala Lumpur, Malaysia; Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
  • 17 The Global Microbiome Conservancy (GMbC); Centre for Innovation in Medical Engineering, University of Malaya, Kuala Lumpur, Malaysia; Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
  • 18 The Global Microbiome Conservancy (GMbC); Department of Medicine, Lagos State University College of Medicine, Lagos, Nigeria
  • 19 The Global Microbiome Conservancy (GMbC); National Institute of Allergy and Infectious Diseases (NIAID), Rockville, MD, USA; National Reference Laboratory, Kigali, Rwanda
  • 20 The Global Microbiome Conservancy (GMbC); National Reference Laboratory, Kigali, Rwanda; Rwanda FDA and College of Medicine and Health Science of the University of Rwanda, Kigali, Rwanda; Health Science of the University of Rwanda, Kigali, Rwanda
  • 21 Institute of Experimental Medicine, Kiel University and University Schleswig-Holstein, Kiel, Germany; Guest Group Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany; Kiel Metaorganism Center, Kiel University, Kiel, Germany
  • 22 Institute of Clinical Molecular Biology, Kiel University & University Hospital Schleswig-Holstein, Kiel, Germany; Kiel Metaorganism Center, Kiel University, Kiel, Germany
  • 23 Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan; HUN-REN Centre for Ecological Research Institute of Evolution, Budapest 1121, Hungary
  • 24 Broad Institute of Massachusetts Institute of Technology 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
  • 25 The Global Microbiome Conservancy (GMbC); Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. Electronic address: ejalm@mit.edu
  • 26 The Global Microbiome Conservancy (GMbC); Institute of Clinical Molecular Biology, Kiel University & University Hospital Schleswig-Holstein, Kiel, Germany; Kiel Metaorganism Center, Kiel University, Kiel, Germany; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. Electronic address: m.groussin@ikmb.uni-kiel.de
  • 27 The Global Microbiome Conservancy (GMbC); Institute of Clinical Molecular Biology, Kiel University & University Hospital Schleswig-Holstein, Kiel, Germany; Institute of Experimental Medicine, Kiel University and University Schleswig-Holstein, Kiel, Germany; Kiel Metaorganism Center, Kiel University, Kiel, Germany; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. Electronic address: m.poyet@iem.uni-kiel.de
Cell, 2026 Nov 02.
PMID: 42971204 DOI: 10.1016/j.cell.2026.10.014

Abstract

Whether human-associated environments drive adaptive genome evolution in gut commensal bacteria remains largely unknown. Here, we investigate how genomic adaptation in gut bacteria differs between industrialized and non-industrialized human populations. We generated a collection of isolate genomes spanning diverse host geographies, lifestyles, species, and strains. We first found that, compared with metagenome-assembled genomes (MAGs), paired isolate genomes recover more functional elements and signals of horizontal gene transfer (HGT). Leveraging isolate genomes from multiple species, we find that strains from industrialized hosts experience an expansion of proteome size and harbor greater pangenome fluidity, driven by recent HGT events. Gene- and variant-level analyses reveal convergent patterns of lifestyle-specific adaptation in functions that are critical for ecological adaptation, such as the stress response, cell-envelope remodeling, and central metabolism. Our results demonstrate that industrialization drives convergent genome evolution in gut bacteria, providing a framework for understanding the mechanisms of microbial adaptation to rapidly changing human environments.

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

Similar publications