Recombination-mediated gene-specific sweeps in motion across the human gut microbiome

References

[1] Moeller AH,Caro-Quintero A,Mjungu D.et al. Cospeciation of gut microbiota with hominids Science 2016 353 380 2 PMC4995445

[2] Suzuki TA,Fitzstevens JL,Schmidt VT.et al. Codiversification of gut microbiota with humans Science 2022 377 1328 32 PMC10777373

[3] N'Guessan A,Brito IL,Serohijos AWR,Shapiro BJ. Mobile gene sequence evolution within individual human gut microbiomes is better explained by gene-specific than host-specific selective pressures Genome Biol Evol 2021 13 PMC8358218

[4] Groussin M,Poyet M,Sistiaga A.et al. Elevated rates of horizontal gene transfer in the industrialized human microbiome Cell 2021 184 2053 2067.e18

[5] Wolff R,Garud NR. Gene-specific selective sweeps are pervasive across human gut microbiomes Nature 2026 650 710 7 PMC12916291

[6] Foley MH,Cockburn DW,Koropatkin NM. The Sus operon: a model system for starch uptake by the human gut Bacteroidetes Cell Mol Life Sci 2016 73 2603 17 PMC4924478

[7] 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 2020 86 PMC7480380

[8] Arnold AR,Chassaing B. Maltodextrin, modern stressor of the intestinal environment Cell Mol Gastroenterol Hepatol 2019 7 475 6 PMC6409436

[9] Sonnenburg ED,Smits SA,Tikhonov M,Higginbottom SK,Wingreen NS,Sonnenburg JL. Diet-induced extinctions in the gut microbiota compound over generations Nature 2016 529 212 5 PMC4850918

[10] Marinos G,Moors KA,Schlicht K.et al. Genome-scale metabolic models predict diet- and lifestyle-driven shifts of ecological interactions in the gut microbiome Gut Microbes 2026 18 2694811 PMC13336287

[11] Sonnenburg ED,Sonnenburg JL. The ancestral and industrialized gut microbiota and implications for human health Nat Rev Microbiol 2019 17 383 90

[12] Martínez I,Stegen JC,Maldonado-Gómez MX.et al. The gut microbiota of rural Papua new Guineans: composition, diversity patterns, and ecological processes Cell Rep 2015 11 527 38

[13] Modi SR,Collins JJ,Relman DA. Antibiotics and the gut microbiota J Clin Invest 2014 124 4212 8 PMC4191029

[14] Chassaing B,Koren O,Goodrich JK.et al. Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome Nature 2015 519 92 6 PMC4910713

[15] Suez J,Korem T,Zeevi D.et al. Artificial sweeteners induce glucose intolerance by altering the gut microbiota Nature 2014 514 181 6

[16] De Filippo C,Cavalieri D,Di Paola M.et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa Proc Natl Acad Sci U S A 2010 107 14691 6 PMC2930426

[17] Harrow GL,Lees JA,Hanage WP.et al. Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures ISME J 2021 15 1523 38 PMC8115253

[18] Harris KB,Flynn KM,Cooper VS. Polygenic adaptation and clonal interference enable sustained diversity in experimental pseudomonas aeruginosa populations Mol Biol Evol 2021 38 5359 75 PMC8662654

[19] Ni M,Junker K,Liu Y.et al. Epigenetic phase variation in the gut microbiome enhances bacterial adaptation Cell Host Microbe 2026 34 1033 1049.e8 PMC13196444

[20] Sanna S,van Zuydam NR,Mahajan A.et al. Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases Nat Genet 2019 51 600 5 PMC6441384