{"id":874373,"date":"2026-10-07T21:16:11","date_gmt":"2026-10-07T21:16:11","guid":{"rendered":"https:\/\/www.newsbeep.com\/us\/874373\/"},"modified":"2026-10-07T21:16:11","modified_gmt":"2026-10-07T21:16:11","slug":"prehistoric-global-migration-of-vanishing-gut-microbes-with-humans","status":"publish","type":"post","link":"https:\/\/www.newsbeep.com\/us\/874373\/","title":{"rendered":"Prehistoric global migration of vanishing gut microbes with humans"},"content":{"rendered":"

Sommer, F. & B\u00e4ckhed, F. The gut microbiota \u2014 masters of host development and physiology. Nat. Rev. Microbiol. 11, 227\u2013238 (2013).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Sanders, J. G. et al. Widespread extinctions of co-diversified primate gut bacterial symbionts from humans. Nat. Microbiol. 8, 1039\u20131050 (2023).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Carter, M. M. et al. Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell 186, 3111\u20133124 (2023).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Sonnenburg, J. L. & Sonnenburg, E. D. Vulnerability of the industrialized microbiota. Science 366, eaaw9255 (2019).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Blaser, M. J. The theory of disappearing microbiota and the epidemics of chronic diseases. Nat. Rev. Immunol. 17, 461\u2013463 (2017).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Suzuki, T. A. et al. Codiversification of gut microbiota with humans. Science 377, 1328\u20131332 (2022).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Moeller, A. H. et al. Cospeciation of gut microbiota with hominids. Science 353, 380\u2013382 (2016).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Amato, K. R. & Carmody, R. N. Gut microbial intersections with human ecology and evolution. Annu. Rev. Anthropol. 52, 295\u2013311 (2023).<\/p>\n

Article<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Nyholm, S. V. & McFall-Ngai, M. J. The winnowing: establishing the squid\u2013vibrio symbiosis. Nat. Rev. Microbiol. 2, 632\u2013642 (2004).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Moran, N. A., McCutcheon, J. P. & Nakabachi, A. Genomics and evolution of heritable bacterial symbionts. Annu. Rev. Genet. 42, 165\u2013190 (2008).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Wibowo, M. C. et al. Reconstruction of ancient microbial genomes from the human gut. Nature 594, 234\u2013239 (2021).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Moodley, Y. et al. The peopling of the Pacific from a bacterial perspective. Science 323, 527\u2013530 (2009).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Linz, B. et al. An African origin for the intimate association between humans and Helicobacter pylori. Nature 445, 915\u2013918 (2007).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Falush, D. et al. Traces of human migrations in Helicobacter pylori populations. Science 299, 1582\u20131585 (2003).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Moeller, A. H., Sanders, J. G., Sprockett, D. D. & Landers, A. Assessing co-diversification in host-associated microbiomes. J. Evol. Biol. 36, 1659\u20131668 (2023).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Amato, K. R. et al. Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME J. 13, 576\u2013587 (2019).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Ochman, H. et al. Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biol. 8, e1000546 (2010).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Perez-Lamarque, B. & Morlon, H. Distinguishing cophylogenetic signal from phylogenetic congruence clarifies the interplay between evolutionary history and species interactions. Syst. Biol. 73, 613\u2013622 (2024).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Good, B. H. Limited codiversification of the gut microbiota with humans. mBio 17, e03727-25 (2026).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Washburne, A. D. et al. Methods for phylogenetic analysis of microbiome data. Nat. Microbiol. 3, 652\u2013661 (2018).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Yahara, K. et al. Chromosome painting in silico in a bacterial species reveals fine population structure. Mol. Biol. Evol. 30, 1454\u20131464 (2013).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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\u20139075 (2015).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Milkman, R. & Bridges, M. M. Molecular evolution of the Escherichia coli chromosome. III. Clonal frames. Genetics 126, 505\u2013517 (1990).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Qin, J. et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55\u201360 (2012).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Li, J. et al. An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32, 834\u2013841 (2014).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207\u2013214 (2012).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Beghini, F. et al. Gut microbiome strain-sharing within isolated village social networks. Nature 637, 167\u2013175 (2025).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Valles-Colomer, M. et al. The person-to-person transmission landscape of the gut and oral microbiomes. Nature 614, 125\u2013135 (2023).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Yu, X. A. et al. Genome-wide sweeps create fundamental ecological units in the human gut microbiome. Nature 655, 202\u2013209 (2026).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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\u2013834 (2019).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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\u20131428 (2019).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Soares, P. et al. The expansion of mtDNA haplogroup L3 within and out of Africa. Mol. Biol. Evol. 29, 915\u2013927 (2012).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Bennett, M. R. et al. Evidence of humans in North America during the Last Glacial Maximum. Science 373, 1528\u20131531 (2021).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Jouganous, J., Long, W., Ragsdale, A. P. & Gravel, S. Inferring the joint demographic history of multiple populations: beyond the diffusion approximation. Genetics 206, 1549\u20131567 (2017).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Fragiadakis, G. K. et al. Links between environment, diet, and the hunter-gatherer microbiome. Gut Microbes 10, 216\u2013227 (2019).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Smits, S. A. et al. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. Science 357, 802\u2013806 (2017).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Ragsdale, A. P. et al. A weakly structured stem for human origins in Africa. Nature 617, 755\u2013763 (2023).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Li, F. et al. Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation. Cell 188, 1226\u20131247 (2025).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Medina-Mu\u00f1oz, S. G. et al. Demographic modeling of admixed Latin American populations from whole genomes. Am. J. Hum. Genet. 110, 1804\u20131816 (2023).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Gurven, M. et al. The Tsimane Health and Life History Project: integrating anthropology and biomedicine. Evol. Anthropol. 26, 54\u201373 (2017).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Chen, S. Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta 2, e107 (2023).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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

Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A. & Korobeynikov, A. Using SPAdes DE Novo Assembler. Curr. Protoc. Bioinform. 70, e102 (2020).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

More, S. & More, A. Assessment the quality of genome assemblies by using QUAST tool for metagenomics. Int. J. Recent Technol. Eng. 8, 4253\u20134259 (2020).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

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

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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\u20131055 (2015).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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\u2013731 (2017).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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\u20131927 (2019).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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\u20132868 (2017).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Varghese, N. J. et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res. 43, 6761\u20136771 (2015).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 119 (2010).<\/p>\n

Article<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Novichkov, V., Kaznadzey, A., Alexandrova, N. & Kaznadzey, D. NSimScan: DNA comparison tool with increased speed, sensitivity and accuracy. Bioinformatics 32, 2380\u20132381 (2016).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Almeida, A. et al. A new genomic blueprint of the human gut microbiota. Nature 568, 499\u2013504 (2019).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Steinegger, M. & S\u00f6ding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026\u20131028 (2017).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

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

Carter, M. M. Prehistoric global migration of vanishing gut microbes with humans [Computer software]. Zenodo https:\/\/doi.org\/10.5281\/zenodo.21206858<\/a> (2026).<\/p>\n","protected":false},"excerpt":{"rendered":"Sommer, F. & B\u00e4ckhed, F. The gut microbiota \u2014 masters of host development and physiology. Nat. Rev. Microbiol.…\n","protected":false},"author":2,"featured_media":874374,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[34],"tags":[368106,97,1159,23165,14377,1160,79],"class_list":["post-874373","post","type-post","status-publish","format-standard","has-post-thumbnail","category-health","tag-bacterial-evolution","tag-health","tag-humanities-and-social-sciences","tag-metagenomics","tag-microbiome","tag-multidisciplinary","tag-science"],"_links":{"self":[{"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/posts\/874373","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/comments?post=874373"}],"version-history":[{"count":0,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/posts\/874373\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/media\/874374"}],"wp:attachment":[{"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/media?parent=874373"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/categories?post=874373"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/tags?post=874373"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}