{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T10:53:24Z","timestamp":1791456804907,"version":"4.3.4"},"posted":{"date-parts":[[2026,10,4]]},"group-title":"Evolutionary Biology","reference-count":73,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T00:00:00Z","timestamp":1791072000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Institutes of Health","award":["R35 GM138284"],"award-info":[{"award-number":["R35 GM138284"]}]},{"name":"National Institutes of Health","award":["R01 DK139214"],"award-info":[{"award-number":["R01 DK139214"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,10,4]]},"abstract":"<jats:title>Summary Paragraph<\/jats:title>\n                <jats:p>\n                  Diet exerts selection on bacterial species within the mammalian gut microbiota\n                  <jats:sup>1,2,3,4,5<\/jats:sup>\n                  , but the extent, modes, genomic bases, and repeatability of gut bacterial adaptive evolution in response to dietary variation within hosts are poorly understood. Here, we show that within-host dietary transitions drive ubiquitous and highly reproducible adaptive evolution of gut bacterial populations. We deeply profiled allele-frequency dynamics in gut microbiota of an experimental cohort of litter-matched wild-derived isogenic mice either transitioned from low-fat\/high-carbohydrate diets to high-fat\/low-carbohydrate diets or maintained on their ancestral low-fat\/high-carbohydrate diet. Dietary transitions induced significantly parallel allele-frequency changes across replicates in 61\/62 core gut bacterial species within five months, whereas 0\/62 species displayed significant across-replicate parallelism in the control group, indicating deterministic adaptive evolutionary responses across the gut microbiota. Adaptation proceeded through multiple modes, including strain sorting and gene-wise responses. The latter were enriched in a subset of gene families and functions across bacterial species, including invertases. Culturing revealed an invertible DNA switch in\n                  <jats:italic>Phocaeicola sartorii<\/jats:italic>\n                  that, in all replicates transitioned to high-fat\/low-carbohydrate diets, localized a promoter sequence upstream of cell-surface glycan foraging genes. These findings elucidate widespread gut bacterial adaptive evolution mediated by within-host dietary variation.\n                <\/jats:p>","DOI":"10.64898\/2026.10.01.755998","type":"posted-content","created":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T03:50:11Z","timestamp":1791172211000},"source":"Crossref","is-referenced-by-count":0,"title":["Community-wide adaptive evolution of gut bacteria during dietary transitions"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9577-6626","authenticated-orcid":false,"given":"Samantha G.","family":"Hernandez","sequence":"first","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, Cornell University; Ithaca, NY, USA"},{"name":"Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ, USA"},{"name":"Department of Microbiology and Immunology, Stanford University School of Medicine; Stanford, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9604-6959","authenticated-orcid":false,"given":"Siddharth","family":"Uppal","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong-Min","family":"Jin","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abigail A.","family":"Landers","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathaniel","family":"Ennis","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2620-7555","authenticated-orcid":false,"given":"Daniel D.","family":"Sprockett","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, Cornell University; Ithaca, NY, USA"},{"name":"Department of Microbiology and Immunology, Wake Forest University School of Medicine; Winston-Salem, NC, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8377-4647","authenticated-orcid":false,"given":"Andrew H.","family":"Moeller","sequence":"additional","affiliation":[{"name":"Department of Ecology and Evolutionary Biology, Cornell University; Ithaca, NY, USA"},{"name":"Department of Ecology and Evolutionary Biology, Princeton University; Princeton, NJ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026100803200797000_2026.10.01.755998v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/nature12820"},{"key":"2026100803200797000_2026.10.01.755998v1.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2014.11.010"},{"key":"2026100803200797000_2026.10.01.755998v1.3","doi-asserted-by":"publisher","DOI":"10.1126\/science.1223813"},{"key":"2026100803200797000_2026.10.01.755998v1.4","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2022.01.002"},{"key":"2026100803200797000_2026.10.01.755998v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2021.02.001"},{"key":"2026100803200797000_2026.10.01.755998v1.6","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3000102"},{"key":"2026100803200797000_2026.10.01.755998v1.7","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.02.015"},{"key":"2026100803200797000_2026.10.01.755998v1.8","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2019.03.007"},{"key":"2026100803200797000_2026.10.01.755998v1.9","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-025-08781-x"},{"key":"2026100803200797000_2026.10.01.755998v1.10","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2020.01.037"},{"key":"2026100803200797000_2026.10.01.755998v1.11","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms9945"},{"key":"2026100803200797000_2026.10.01.755998v1.12","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-33412-8"},{"key":"2026100803200797000_2026.10.01.755998v1.13","doi-asserted-by":"publisher","DOI":"10.1016\/J.CHOM.2021.08.003"},{"key":"2026100803200797000_2026.10.01.755998v1.14","doi-asserted-by":"publisher","DOI":"10.1101\/gr.265058.120"},{"key":"2026100803200797000_2026.10.01.755998v1.15","doi-asserted-by":"publisher","DOI":"10.1101\/gr.276306.121"},{"key":"2026100803200797000_2026.10.01.755998v1.16","doi-asserted-by":"crossref","first-page":"1829","DOI":"10.1038\/s41564-025-02036-1","article-title":"Within-host bacterial evolution and the emergence of pathogenicity","volume":"10","year":"2025","journal-title":"Nat. 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