Sommer, F. & Bäckhed, F. The gut microbiota — masters of host development and physiology. Nat. Rev. Microbiol. 11, 227–238 (2013).

Article 
CAS 
PubMed 

Google Scholar
 

Sanders, J. G. et al. Widespread extinctions of co-diversified primate gut bacterial symbionts from humans. Nat. Microbiol. 8, 1039–1050 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Carter, M. M. et al. Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell 186, 3111–3124 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Sonnenburg, J. L. & Sonnenburg, E. D. Vulnerability of the industrialized microbiota. Science 366, eaaw9255 (2019).

Article 
CAS 
PubMed 

Google Scholar
 

Blaser, M. J. The theory of disappearing microbiota and the epidemics of chronic diseases. Nat. Rev. Immunol. 17, 461–463 (2017).

Article 
CAS 
PubMed 

Google Scholar
 

Sprockett, D. D. et al. Microbiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon. Nat. Commun. 11, 3772 (2020).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Suzuki, T. A. et al. Codiversification of gut microbiota with humans. Science 377, 1328–1332 (2022).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Moeller, A. H. et al. Cospeciation of gut microbiota with hominids. Science 353, 380–382 (2016).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Amato, K. R. & Carmody, R. N. Gut microbial intersections with human ecology and evolution. Annu. Rev. Anthropol. 52, 295–311 (2023).

Article 

Google Scholar
 

Nyholm, S. V. & McFall-Ngai, M. J. The winnowing: establishing the squid–vibrio symbiosis. Nat. Rev. Microbiol. 2, 632–642 (2004).

Article 
CAS 
PubMed 

Google Scholar
 

Moran, N. A., McCutcheon, J. P. & Nakabachi, A. Genomics and evolution of heritable bacterial symbionts. Annu. Rev. Genet. 42, 165–190 (2008).

Article 
CAS 
PubMed 

Google Scholar
 

Wibowo, M. C. et al. Reconstruction of ancient microbial genomes from the human gut. Nature 594, 234–239 (2021).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Moodley, Y. et al. The peopling of the Pacific from a bacterial perspective. Science 323, 527–530 (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 445, 915–918 (2007).

Article 
ADS 
PubMed 
PubMed Central 

Google Scholar
 

Falush, D. et al. Traces of human migrations in Helicobacter pylori populations. Science 299, 1582–1585 (2003).

Article 
ADS 
CAS 
PubMed 

Google Scholar
 

Thorpe, H. A. et al. Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations. Nat. Commun. 13, 6842 (2022).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Mah, J. C., Lohmueller, K. E. & Garud, N. R. Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history. Mol. Biol. Evol. 42, msaf010 (2025).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Moeller, A. H., Sanders, J. G., Sprockett, D. D. & Landers, A. Assessing co-diversification in host-associated microbiomes. J. Evol. Biol. 36, 1659–1668 (2023).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Nishida, A. H. & Ochman, H. Captivity and the co-diversification of great ape microbiomes. Nat. Commun. 12, 5632 (2021).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Amato, K. R. et al. Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME J. 13, 576–587 (2019).

Article 
CAS 
PubMed 

Google Scholar
 

Ochman, H. et al. Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biol. 8, e1000546 (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. Syst. Biol. 73, 613–622 (2024).

Article 
PubMed 

Google Scholar
 

Good, B. H. Limited codiversification of the gut microbiota with humans. mBio 17, e03727-25 (2026).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Washburne, A. D. et al. Methods for phylogenetic analysis of microbiome data. Nat. Microbiol. 3, 652–661 (2018).

Article 
CAS 
PubMed 

Google Scholar
 

Sakoparnig, T., Field, C. & van Nimwegen, E. Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species. eLife 10, e65366 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Yahara, K. et al. Chromosome painting in silico in a bacterial species reveals fine population structure. Mol. Biol. Evol. 30, 1454–1464 (2013).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Abdill, R. J., Adamowicz, E. M. & Blekhman, R. Public human microbiome data are dominated by highly developed countries. PLoS Biol. 20, e3001536 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Dixit, P. D., Pang, T. Y., Studier, F. W. & Maslov, S. Recombinant transfer in the basic genome of Escherichia coli. Proc. Natl Acad. Sci. USA 112, 9070–9075 (2015).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Milkman, R. & Bridges, M. M. Molecular evolution of the Escherichia coli chromosome. III. Clonal frames. Genetics 126, 505–517 (1990).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Qin, J. et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55–60 (2012).

Article 
ADS 
CAS 
PubMed 

Google Scholar
 

Li, J. et al. An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32, 834–841 (2014).

Article 
CAS 
PubMed 

Google Scholar
 

The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012).

Article 
ADS 

Google Scholar
 

Beghini, F. et al. Gut microbiome strain-sharing within isolated village social networks. Nature 637, 167–175 (2025).

Article 
ADS 
CAS 
PubMed 

Google Scholar
 

Valles-Colomer, M. et al. The person-to-person transmission landscape of the gut and oral microbiomes. Nature 614, 125–135 (2023).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Yu, X. A. et al. Genome-wide sweeps create fundamental ecological units in the human gut microbiome. Nature 655, 202–209 (2026).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Arevalo, P., VanInsberghe, D., Elsherbini, J., Gore, J. & Polz, M. F. A reverse ecology approach based on a biological definition of microbial populations. Cell 178, 820–834 (2019).

Article 
CAS 
PubMed 

Google Scholar
 

Haber, M. et al. A rare deep-rooting D0 African Y-chromosomal haplogroup and its implications for the expansion of modern humans out of Africa. Genetics 212, 1421–1428 (2019).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Soares, P. et al. The expansion of mtDNA haplogroup L3 within and out of Africa. Mol. Biol. Evol. 29, 915–927 (2012).

Article 
CAS 
PubMed 

Google Scholar
 

Potter, B. A. et al. Current evidence allows multiple models for the peopling of the Americas. Sci. Adv. 4, eaat5473 (2018).

Article 
ADS 
PubMed 
PubMed Central 

Google Scholar
 

Bennett, M. R. et al. Evidence of humans in North America during the Last Glacial Maximum. Science 373, 1528–1531 (2021).

Article 
ADS 
CAS 
PubMed 

Google Scholar
 

Jouganous, J., Long, W., Ragsdale, A. P. & Gravel, S. Inferring the joint demographic history of multiple populations: beyond the diffusion approximation. Genetics 206, 1549–1567 (2017).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Fragiadakis, G. K. et al. Links between environment, diet, and the hunter-gatherer microbiome. Gut Microbes 10, 216–227 (2019).

Article 
CAS 
PubMed 

Google Scholar
 

Smits, S. A. et al. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. Science 357, 802–806 (2017).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Ragsdale, A. P. et al. A weakly structured stem for human origins in Africa. Nature 617, 755–763 (2023).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Li, F. et al. Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation. Cell 188, 1226–1247 (2025).

Article 
CAS 
PubMed 

Google Scholar
 

Medina-Muñoz, S. G. et al. Demographic modeling of admixed Latin American populations from whole genomes. Am. J. Hum. Genet. 110, 1804–1816 (2023).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Ragsdale, A. P. & Gravel, S. Models of archaic admixture and recent history from two-locus statistics. PLoS Genet. 15, e1008204 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Pico, T., Mitrovica, J. X. & Mix, A. C. Sea level fingerprinting of the Bering Strait flooding history detects the source of the Younger Dryas climate event. Sci. Adv. 6, eaay2935 (2020).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Gurven, M. et al. The Tsimane Health and Life History Project: integrating anthropology and biomedicine. Evol. Anthropol. 26, 54–73 (2017).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Chen, S. Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta 2, e107 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Babraham Bioinformatics. FastQC: a quality control tool for high throughput sequence data. v.0.12.0 http://www.bioinformatics.babraham.ac.uk/projects/fastqc/(Babraham Institute, 2023).

Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A. & Korobeynikov, A. Using SPAdes DE Novo Assembler. Curr. Protoc. Bioinform. 70, e102 (2020).

Article 
CAS 

Google Scholar
 

Aroney, S. T. N. et al. CoverM: read alignment statistics for metagenomics. Bioinformatics 41, btaf147 https://doi.org/10.1093/bioinformatics/btaf147 (2025).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

More, S. & More, A. Assessment the quality of genome assemblies by using QUAST tool for metagenomics. Int. J. Recent Technol. Eng. 8, 4253–4259 (2020).


Google Scholar
 

Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Bowers, R. M. et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725–731 (2017).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925–1927 (2019).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864–2868 (2017).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9, 5114 (2018).

Article 
ADS 
PubMed 
PubMed Central 

Google Scholar
 

Varghese, N. J. et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res. 43, 6761–6771 (2015).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Olm, M. R. et al. Consistent metagenome-derived metrics verify and delineate bacterial species boundaries. mSystems 5, e00731-19 (2020).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 119 (2010).

Article 

Google Scholar
 

Novichkov, V., Kaznadzey, A., Alexandrova, N. & Kaznadzey, D. NSimScan: DNA comparison tool with increased speed, sensitivity and accuracy. Bioinformatics 32, 2380–2381 (2016).

Article 
CAS 
PubMed 

Google Scholar
 

Almeida, A. et al. A new genomic blueprint of the human gut microbiota. Nature 568, 499–504 (2019).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).

Article 
CAS 
PubMed 

Google Scholar
 

Carter, M. M. Prehistoric global migration of vanishing gut microbes with humans [Data set]. Zenodo https://doi.org/10.5281/zenodo.21765848 (2026).

Carter, M. M. Prehistoric global migration of vanishing gut microbes with humans [Computer software]. Zenodo https://doi.org/10.5281/zenodo.21206858 (2026).