Garud, N. R., Good, B. H., Hallatschek, O. & Pollard, K. S. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLoS Biol. 17, e3000102 (2019).
Zhao, S. et al. Adaptive evolution within gut microbiomes of healthy people. Cell Host Microbe 25, 656–667 (2019).
Poyet, M. et al. A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research. Nat. Med. 25, 1442–1452 (2019).
Yaffe, E. & Relman, D. A. Tracking microbial evolution in the human gut using hi-c reveals extensive horizontal gene transfer, persistence and adaptation. Nat. Microbiol. 5, 343–353 (2020).
Zlitni, S. et al. Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale. Genome Med. 12, 50 (2020).
Liu, Z. & Good, B. H. Dynamics of bacterial recombination in the human gut microbiome. PLoS Biol. 22, e3002472 (2024).
Smillie, C. S. et al. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480, 241–244 (2011).
Groussin, M. et al. Elevated rates of horizontal gene transfer in the industrialized human microbiome. Cell 184, 2053–2067 (2021).
McInnes, R. S., McCallum, G. E., Lamberte, L. E. & van Schaik, W. Horizontal transfer of antibiotic resistance genes in the human gut microbiome. Curr. Opin. Microbiol. 53, 35–43 (2020).
Shapiro, B. J. et al. Population genomics of early events in the ecological differentiation of bacteria. Science 336, 48–51 (2012).
Shapiro, B. J. & Polz, M. F. Ordering microbial diversity into ecologically and genetically cohesive units. Trends Microbiol. 22, 235–247 (2014).
Hudson, R. R., Bailey, K., Skarecky, D., Kwiatowski, J. & Ayala, F. J. Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster. Genetics 136, 1329–1340 (1994).
Vitti, J. J., Grossman, S. R. & Sabeti, P. C. Detecting natural selection in genomic data. Annu. Rev. Genet. 47, 97–120 (2013).
Sabeti, P. C. et al. Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832–837 (2002).
Voight, B. F., Kudaravalli, S., Wen, X. & Pritchard, J. K. A map of recent positive selection in the human genome. PLoS Biol. 4, e72 (2006).
Garud, N. R., Messer, P. W., Buzbas, E. O. & Petrov, D. A. Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps. PLoS Genet. 11, e1005004 (2015).
Ferrer-Admetlla, A., Liang, M., Korneliussen, T. & Nielsen, R. On detecting incomplete soft or hard selective sweeps using haplotype structure. Mol. Biol. Evol. 31, 1275–1291 (2014).
Shapiro, B. J. Signatures of natural selection and ecological differentiation in microbial genomes. Adv. Exp. Med. Biol. 781, 339–359 (2014).
Good, B. H., Bhatt, A. S. & McDonald, M. J. Unraveling the tempo and mode of horizontal gene transfer in bacteria. Trends Microbiol. 33, 853–865 (2025).
Pritchard, J. K. & Przeworski, M. Linkage disequilibrium in humans: models and data. Am. J. Hum. Genet. 69, 1–14 (2001).
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).
Eyre-Walker, A. & Keightley, P. D. The distribution of fitness effects of new mutations. Nat. Rev. Genet. 8, 610–618 (2007).
Lawrie, D. S. & Petrov, D. A. Comparative population genomics: power and principles for the inference of functionality. Trends Genet. 30, 133–139 (2014).
Cvijović, I., Good, B. H. & Desai, M. M. The effect of strong purifying selection on genetic diversity. Genetics 209, 1235–1278 (2018).
Hartfield, M. & Otto, S. P. Recombination and hitchhiking of deleterious alleles. Evolution 65, 2421–2434 (2011).
Haller, B. C. & Messer, P. W. SLiM 4: Multispecies eco-evolutionary modeling. Am. Nat. 201, E127–E139 (2023).
Lloyd-Price, J. et al. Strains, functions and dynamics in the expanded human microbiome project. Nature 550, 61–66 (2017).
Xie, H. et al. Shotgun metagenomics of 250 adult twins reveals genetic and environmental impacts on the gut microbiome. Cell Systems 3, 572–584 (2016).
Qin, J. et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55–60 (2012).
Korpela, K. et al. Selective maternal seeding and environment shape the human gut microbiome. Genome Res. 28, 561–568 (2018).
Nayfach, S., Rodriguez-Mueller, B., Garud, N. & Pollard, K. S. An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. Genome Res. 26, 1612–1625 (2016).
Almeida, A. et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nat. Biotechnol. 39, 105–114 (2021).
Shen, E. et al. Subtyping analysis reveals new variants and accelerated evolution of Clostridioides difficile toxin b. Commun. Biol. 3, 347 (2020).
Mansfield, M. J. et al. Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B. PLoS Pathog. 16, e1009181 (2020).
Dingle, K. E. et al. Recombinational switching of the Clostridium difficile S-layer and a novel glycosylation gene cluster revealed by large-scale whole-genome sequencing. J. Infect. Dis. 207, 675–686 (2013).
Steinberg, H. D. & Snitkin, E. S. Homologous recombination in Clostridioides difficile mediates diversification of cell surface features and transport systems. mSphere 5, 10–1128 (2020).
Chen, D. W. & Garud, N. R. Rapid evolution and strain turnover in the infant gut microbiome. Genome Res. 32, 1124–1136 (2022).
Tatusov, R. L., Galperin, M. Y., Natale, D. A. & Koonin, E. V. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33–36 (2000).
Barrett, A. J. Enzyme nomenclature. Recommendations 1992: Supplement 2: Corrections and additions (1994). Eur. J. Biochem. 232, 1 (1995).
Grand, M., Riboulet-Bisson, E., Deutscher, J., Hartke, A. & Sauvageot, N. Enterococcus faecalis maltodextrin gene regulation by combined action of maltose gene regulator MalR and pleiotropic regulator CcpA. Appl. Environ. Microbiol. 86, e01147–20 (2020).
Arnold, A. R. & Chassaing, B. Maltodextrin, modern stressor of the intestinal environment. Cell. Mol. Gastroenterol. Hepatol. 7, 475–476 (2019).
Ze, X., Duncan, S. H., Louis, P. & Flint, H. J. Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J. 6, 1535–1543 (2012).
Shetty, S. A. et al. Inter-species metabolic interactions in an in-vitro minimal human gut microbiome of core bacteria. NPJ Biofilms Microbiomes 8, 21 (2022).
Sonnenburg, J. L. & Sonnenburg, E. D. Vulnerability of the industrialized microbiota. Science 366, eaaw9255 (2019).
Brito, I. L. et al. Mobile genes in the human microbiome are structured from global to individual scales. Nature 535, 435–439 (2016).
Pasolli, E. et al. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell 176, 649–662 (2019).
Obregon-Tito, A. J. et al. Subsistence strategies in traditional societies distinguish gut microbiomes. Nat. Commun. 6, 6505 (2015).
Pehrsson, E. C. et al. Interconnected microbiomes and resistomes in low-income human habitats. Nature 533, 212–216 (2016).
Liu, W. et al. Unique features of ethnic Mongolian gut microbiome revealed by metagenomic analysis. Sci. Rep. 6, 34826 (2016).
Rosen, M. J., Davison, M., Bhaya, D. & Fisher, D. S. Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche. Science 348, 1019–1023 (2015).
Sakoparnig, T., Field, C. & van Nimwegen, E. Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species. eLife 10, e65366 (2021).
Hehemann, J.-H. et al. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464, 908–912 (2010).
Tourrette, E. et al. An ancient ecospecies of Helicobacter pylori. Nature 635, 178–185 (2024).
Stolyarova, A. V. et al. Complex fitness landscape shapes variation in a hyperpolymorphic species. eLife 11, e76073 (2022).
Arnold, B. et al. Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen. Mol. Biol. Evol. 37, 417–428 (2020).
Crits-Christoph, A., Olm, M. R., Diamond, S., Bouma-Gregson, K. & Banfield, J. F. Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow. ISME J. 14, 1834–1846 (2020).
Callahan, B., Neher, R. A., Bachtrog, D., Andolfatto, P. & Shraiman, B. I. Correlated evolution of nearby residues in drosophilid proteins. PLoS Genet. 7, e1001315 (2011).
Rocha, E. P. & Feil, E. J. Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria?. PLoS Genet. 6, e1001104 (2010).
Schloissnig, S. et al. Genomic variation landscape of the human gut microbiome. Nature 493, 45–50 (2013).
Assaf, Z. J., Petrov, D. A. & Blundell, J. R. Obstruction of adaptation in diploids by recessive, strongly deleterious alleles. Proc. Natl Acad. Sci. USA 112, E2658–E2666 (2015).
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).
Liu, B., Zheng, D., Zhou, S., Chen, L. & Yang, J. VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res. 50, D912–D917 (2022).
Lack, J. B. et al. The Drosophila Genome Nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population. Genetics 199, 1229–1241 (2015).
Wolff, R. & Garud, N. Gene-specific selective sweeps are pervasive across human gut microbiomes. Dryad https://datadryad.org/dataset/doi:10.5061/dryad.9ghx3ffx4 (2025).
Wolff, R. & Garud, N. Gene-specific selective sweeps are pervasive across human gut microbiomes. Zenodo https://doi.org/10.5281/zenodo.17253586 (2025).
Gangwer, K. A. et al. Molecular evolution of the Helicobacter pylori vacuolating toxin gene vacA. J. Bacteriol. 192, 6126–6135 (2010).