Cited by 210Gut microbiota and healthGenomics and Phylogenetic StudiesEvolution and Genetic Dynamics

Codiversification of gut microbiota with humans

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Suzuki, Taichi A., Fitzstevens, J. Liam, Schmidt, Victor T., Enav, Hagay, Huus, Kelsey E., Mbong Ngwese, Mirabeau, Grießhammer, Anne, Pfleiderer, Anne +17 more·2022·Science

Published version of a preprint

Abstract

The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia, and Africa, including mothers and their children. Between and within countries, a parallel evolutionary history was evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes.

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  • Multiple bacterial species' phylogenies resemble their human host populations' phylogenies, highlighting that geographical stratification in those species is unlikely to be driven by lifestyle alone.

    “Moreover, it has also been observed that multiple bac­ terial species' phylogenies resemble their human host popula­ tions' phylogenies, highlighting that geographical stratification in those species is unlikely to be driven by lifestyle alone. 15”
  • Clostridiales is part of the phylum Bacillota, which was previously observed to be the top phylum showing co-diversification with human populations.

    “Interestingly, Clostridiales is part of the phylum Bacillota (formerly known as Firmicutes), which was previously observed to be the top phylum showing co-diversification with human populations.”

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Research works printed but not linked: 2

  1. [6]Merrill BD bioRxiv 2022.03.30.486478 [ Preprint] (2022). 10.1101/2022.03.30.48647. · DOI
  2. [26]Tung J eLife 4, e05224 (2015).25774601

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Authors
Suzuki, T. A., Fitzstevens, J. L., Schmidt, V. T., Enav, H., Huus, K. E., Mbong Ngwese, M., Grießhammer, A., Pfleiderer, A., Adegbite, B. R., Zinsou, J. F., Esen, M., Velavan, T. P., Adegnika, A. A., Song, L. H., Spector, T. D., Muehlbauer, A. L., Marchi, N., Kang, H., Maier, L., Blekhman, R., Ségurel, L., Ko, G., Youngblut, N. D., Kremsner, P., & Ley, R. E.
Affiliations
  • Max Planck Institute for Biology (DE)
  • Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany.
  • University of Tübingen (DE)
  • Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany.
  • Centre de Recherche Médicales de Lambaréné (GA)
  • German Center for Infection Research (DE)
  • Vietnamese - German Center of Excellence in Medical Research (VN)
  • Vietnamese German Center for Medical Research, Hanoi, Vietnam.
  • Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK.
  • University of Minnesota (US)
  • Centre National de la Recherche Scientifique (FR)
  • Seoul National University (KR)
  • Lyon 1 Université (FR)
Corresponding author
  • Suzuki, Taichi A.
  • Fitzstevens, J. Liam
  • Ley, Ruth E.
Venue
Science
Published
2022-09-16
Volume
377
Issue
6612
Pages
1328-1332
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
OpenAlex
W4296032784
Cited by
210
References
95
Citations by year
2026: 48 · 2025: 53 · 2024: 52 · 2023: 48 · 2022: 9
FWCI
13.23
Type
journal article
Language
en
Open access
Licence
cc-by-nc-nd
Locations
  • Science (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion, public-domain)
  • HAL (submittedVersion, other-oa)
  • Pure Amsterdam UMC (submittedVersion)
Funders
  • Wellcome Trust
  • National Institute for Health and Care Research
  • King's College London
  • European Commission
  • Agence Nationale de la Recherche (ANR-15-CE02-0003)
  • Max-Planck-Gesellschaft
  • National Institutes of Health
  • Medical Research Council
  • National Institute of General Medical Sciences (R35GM128716)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords
gut microbiota, co-diversification, core microbiome, host dependency, genome reduction, oxygen sensitivity, temperature sensitivity, mother-child pairs, gut metagenomics, human genome
MeSH terms
Gastrointestinal Microbiome, Host Microbial Interactions, Bacteria, Child, Humans, Oxygen, Metagenome

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