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Codiversification of gut microbiota with humans
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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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“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”
From Global genetic diversity of human gut microbiome species is related to geographic location and host health (2025) · cites this paper as [15]
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“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.”
From Global genetic diversity of human gut microbiome species is related to geographic location and host health (2025) · cites this paper as [15]
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Metadata
- 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.
- ORCID
- Suzuki, Taichi A.
- Fitzstevens, J. Liam
- Schmidt, Victor T.
- Enav, Hagay
- Huus, Kelsey E.
- Mbong Ngwese, Mirabeau
- Grießhammer, Anne
- Pfleiderer, Anne
- Adegbite, Bayode R.
- Zinsou, Jeannot F.
- Esen, Meral
- Velavan, Thirumalaisamy P.
- Adegnika, Ayola A.
- Song, Le Huu
- Spector, Timothy D.
- Muehlbauer, Amanda L.
- Marchi, Nina
- Kang, Hyena
- Maier, Lisa
- Blekhman, Ran
- Ségurel, Laure
- Ko, GwangPyo
- Youngblut, Nicholas D.
- Kremsner, Peter
- Ley, Ruth E.
- Venue
- Science
- Published
- 2022-09-16
- Volume
- 377
- Issue
- 6612
- Pages
- 1328-1332
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC10777373
- 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
- green
- doi.org
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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