Prehistoric global migration of endangered gut microbes with humans

  • Sommer, F. & Bäckhed, F. The gut microbiota – masters of host development and physiology. Nat. Reverend Microbiol. 11227-238 (2013).

    Article CAS PubMed Google Scholar

  • Sanders, JG et al. Widespread extinctions of primate co-diversified gut bacterial symbionts in humans. Nat. Microbiol. 81039-1050 (2023).

    Article CAS PubMed PubMed Central Google Scholar

  • Carter, MM et al. Hadza hunter-gatherer ultra-deep sequencing recovers disappearing gut microbes. Cell 1863111-3124 (2023).

    Article CAS PubMed PubMed Central Google Scholar

  • Sonnenburg, JL & Sonnenburg, ED Vulnerability of industrialized microbiota. Science 366eaaw9255 (2019).

    Article CAS PubMed Google Scholar

  • Blaser, MJ The disappearing microbiota theory and chronic disease epidemics. Nat. Reverend Immunol. 17461-463 (2017).

    Article CAS PubMed Google Scholar

  • Sprockett, DD et al. Assembly, structure and dynamics of the microbiota among Tsimane horticulturists of the Bolivian Amazon. Nat. Common. 113772 (2020).

    Article ADS CAS PubMed PubMed Central Google Scholar

  • Suzuki, TA et al. Codiversification of the intestinal microbiota with humans. Science 3771328-1332 (2022).

    Article ADS CAS PubMed PubMed Central Google Scholar

  • Moeller, AH et al. Cospeciation of the intestinal microbiota with hominids. Science 353380-382 (2016).

    Article ADS CAS PubMed PubMed Central Google Scholar

  • Amato, KR & Carmody, RN Gut microbial intersections with human ecology and evolution. Ann. Reverend Anthropol. 52295-311 (2023).

    Google Scholar article

  • Nyholm, SV & McFall-Ngai, MJ Winnowing: establishing the squid–vibrio symbiosis. Nat. Reverend Microbiol. 2632-642 (2004).

    Article CAS PubMed Google Scholar

  • Moran, NA, McCutcheon, JP & Nakabachi, A. Genomics and evolution of heritable bacterial symbionts. Ann. Reverend Genet. 42165-190 (2008).

    Article CAS PubMed Google Scholar

  • Wibowo, MC et al. Reconstruction of ancient microbial genomes from the human gut. Nature 594234-239 (2021).

    Article ADS CAS PubMed PubMed Central Google Scholar

  • Moodley, Y. et al. The population of the Pacific from a bacterial point of view. Science 323527-530 (2009).

    Article ADS CAS PubMed PubMed Central Google Scholar

  • Linz, B. et al. An African origin for the intimate association between humans and Helicobacter pylori. Nature 445915-918 (2007).

    Article ADS PubMed PubMed Central Google Scholar

  • Falush, D. et al. Traces of human migrations in Helicobacter pylori populations. Science 2991582-1585 (2003).

    Article ADS CAS PubMed Google Scholar

  • Thorpe, HA et al. The repeated expansions out of Africa of Helicobacter pylori motivated by the replacement of deleterious mutations. Nat. Common. 136842 (2022).

    Article ADS CAS PubMed PubMed Central Google Scholar

  • Mah, JC, Lohmueller, KE & Garud, NR Inference of demographic histories and selective effects of the human gut commensal microbiota throughout human history. Mol. Biol. Evol. 42msaf010 (2025).

    Article CAS PubMed PubMed Central Google Scholar

  • Moeller, AH, Sanders, JG, Sprockett, DD & Landers, A. Assessing co-diversification of host-associated microbiomes. J. Evol. Biol. 361659-1668 (2023).

    Article PubMed PubMed Central Google Scholar

  • Nishida, AH & Ochman, H. Captivity and co-diversification of great ape microbiomes. Nat. Common. 125632 (2021).

    Article ADS CAS PubMed PubMed Central Google Scholar

  • Amato, KR et al. Evolutionary trends in host physiology override dietary niche in structuring primate gut microbiomes. ISME J. 13576-587 (2019).

    Article CAS PubMed Google Scholar

  • Ochman, H. et al. Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biol. 8e1000546 (2010).

    Article PubMed PubMed Central Google Scholar

  • Perez-Lamarque, B. & Morlon, H. Distinguishing cophylogenetic signal from phylogenetic congruence clarifies the interplay between evolutionary history and species interactions. System. Biol. 73613-622 (2024).

    Article PubMed Google Scholar

  • Okay, BH Limited codiversification of the intestinal microbiota with humans. mBio 17e03727-25 (2026).

    Article PubMed PubMed Central Google Scholar

  • Washburne, AD et al. Methods for phylogenetic analysis of microbiome data. Nat. Microbiol. 3652-661 (2018).

    Article CAS PubMed Google Scholar

  • Sakoparnig, T., Field, C. and van Nimwegen, E. Whole-genome phylogenies reflect recombination rate distributions for many bacterial species. eLife 10e65366 (2021).

    Article CAS PubMed PubMed Central Google Scholar

  • Lawson, D.J., Hellenthal, G., Myers, S. & Falush, D. Inferring population structure using dense haplotype data. PLoS Genet. 8e1002453 (2012).

    Article CAS PubMed PubMed Central Google Scholar

  • Yahara, K. et al. In silico chromosome painting in a bacterial species reveals fine population structure. Mol. Biol. Evol. 301454-1464 (2013).

    Article CAS PubMed PubMed Central Google Scholar

  • Liu, Z. & Good, BH Dynamics of bacterial recombination in the human gut microbiome. PLoS Biol. 22e3002472 (2024).

    Article CAS PubMed PubMed Central Google Scholar

  • Abdill, RJ, Adamowicz, EM and Blekhman, R. Public data on the human microbiome are dominated by highly developed countries. PLoS Biol. 20e3001536 (2022).

    Article CAS PubMed PubMed Central Google Scholar

  • Dixit, PD, Pang, TY, Studier, FW & Maslov, S. Recombinant transfer into the core genome of Escherichia coli. Proc. Natl Acad. Sci. USA 1129070-9075 (2015).

    Article ADS CAS PubMed PubMed Central Google Scholar

  • Milkman, R. & Bridges, MM Molecular evolution of Escherichia coli chromosome. III. Clonal frameworks. Genetic 126505-517 (1990).

    Article CAS PubMed PubMed Central Google Scholar

  • Qin, J. et al. A metagenome-wide association study of the gut microbiota in type 2 diabetes. Nature 49055-60 (2012).

    Article ADS CAS PubMed Google Scholar

  • Li, J. et al. An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnology. 32834-841 (2014).

    Article CAS PubMed Google Scholar

  • The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486207-214 (2012).

    Article ADS Google Scholar

  • Beghini, F. et al. Sharing the constraints of the intestinal microbiome within the social networks of isolated villages. Nature 637167-175 (2025).

    Article ADS CAS PubMed Google Scholar

  • Valles-Colomer, M. et al. The landscape of person-to-person transmission of gut and oral microbiomes. Nature 614125-135 (2023).

    Article ADS CAS PubMed PubMed Central Google Scholar

  • Yu, XA et al. Genome-wide analyzes create fundamental ecological units in the human gut microbiome. Nature 655202-209 (2026).

    Article CAS PubMed PubMed Central Google Scholar

  • Arevalo, P., VanInsberghe, D., Elsherbini, J., Gore, J. & Polz, MF A reverse ecology approach based on a biological definition of microbial populations. Cell 178820-834 (2019).

    Article CAS PubMed Google Scholar

  • Haber, M. et al. A rare deep-rooted African Y chromosome D0 haplogroup and its implications for the expansion of modern humans out of Africa. Genetic 2121421-1428 (2019).

    Article PubMed PubMed Central Google Scholar

  • Soares, P. et al. The expansion of mtDNA haplogroup L3 into and out of Africa. Mol. Biol. Evol. 29915-927 (2012).

    Article CAS PubMed Google Scholar

  • Potter, BA et al. Current evidence supports several models for the settlement of the Americas. Sci. Av. 4eat5473 (2018).

    Article ADS PubMed PubMed Central Google Scholar

  • Bennett, MR et al. Evidence of human presence in North America…

  • Gn Health

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