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Codiversification of gut microbiota with humans
Open accessPublished 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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“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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Cites
Classification and Regression by randomForest
Liaw, A. I., & Wiener, M. C. (2007) · Cited by 18,594
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Hyatt, D., Chen, G.-L., LoCascio, P. F., Land, M., Larimer, F. W., & Hauser, L. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-119 · Cited by 12,692
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation
Letunic, I., & Bork, P. (2021) · Nucleic Acids Res. · doi:10.1093/nar/gkab301 · Cited by 9,915
phytools: an R package for phylogenetic comparative biology (and other things)
Revell, L. J. (2011) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2011.00169.x · Cited by 9,336
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Huerta-Cepas, J., Forslund, K., Coelho, L. P., Szklarczyk, D., Jensen, L. J., von Mering, C., & Bork, P. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx148 · Cited by 2,709
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Jia, B., Raphenya, A. R., Alcock, B. P., Waglechner, N., Guo, P., Tsang, K. K., Lago, B. A., Dave, B. M., Pereira, S. K., Sharma, A. N., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1004 · Cited by 2,686
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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
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