Codiversification of gut microbiota with humans

Taichi A. Suzuki, J. Liam Fitzstevens, Victor T. Schmidt, Hagay Enav, Kelsey E. Huus, Mirabeau Mbong Ngwese, Anne Grießhammer, Anne Pfleiderer, Bayode R. Adegbite, Jeannot F. Zinsou, Meral Esen, Thirumalaisamy P. Velavan, Ayola A. Adegnika, Le Huu Song, Timothy D. Spector, Amanda L Muehlbauer, Nina Marchi, Hyena Kang, Lisa Maier, Ran BlekhmanLaure Ségurel, Gwang Pyo Ko, Nicholas D. Youngblut, Peter Kremsner, Ruth E. Ley

Research output: Contribution to journalArticlepeer-review

53 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)1328-1332
Number of pages5
Issue number6612
StatePublished - Sep 16 2022

Bibliographical note

Funding Information:
We thank T. H. Nguyen, E. Cosgrove, A. Clark, A. Kostic, M. Taylor, Native American tribe officers (M. Bremer, J. Aguilar, J. Charlie, R. Williams, B. Lewis, S. Anton, A. Garcia-Lewis, and B. Bernstein), S. Dauser and members of the Department of Microbiome Science, and four anonymous reviewers. Funding: This work was supported by the Max Planck Society. T.D.S. was funded by the Wellcome Trust, Medical Research Council, European Union, Chronic Disease Research Foundation, Zoe Global Ltd., the National Institute for Health Research-funded BioResource, and the Clinical Research Facility and Biomedical Research Centre based at Guy's and St Thomas' NHS Foundation Trust in partnership with King's College London. L.S. was supported by an Agence Nationale de la Recherche grant (MICROREGAL, ANR-15-CE02-0003). R.B. was supported by NIH grant R35-GM128716.

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Copyright © 2022 The Authors.

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