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Horizontal gene transfer driven by temperate phages that can perform lysogeny is also widespread in mammalian intestines. Yet, the roles of mutation and especially lysogeny as key drivers of gut bacterial adaptation remain poorly understood. The mammalian gut contains hundreds of bacterial species, each with many strains and ecotypes, whose abundance varies along the lifetime of a host. A continuous high input of mutations and horizontal gene transfer events mediated by temperate phages drives that diversity. Future experiments to study the interaction between mutations that cause adaptation in microbiomes and lysogenic events with different costs and benefits will be key to understand the dynamic microbiomes of mammals. Also see the video abstract here: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/youtu.be\/Zjqsiyb5Pk0\">https:\/\/youtu.be\/Zjqsiyb5Pk0<\/jats:ext-link><\/jats:p>","DOI":"10.1002\/bies.202300063","type":"journal-article","created":{"date-parts":[[2023,6,25]],"date-time":"2023-06-25T01:22:45Z","timestamp":1687656165000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Ecotype formation and prophage domestication during gut bacterial evolution"],"prefix":"10.1002","volume":"45","author":[{"given":"Nelson","family":"Fraz\u00e3o","sequence":"first","affiliation":[{"name":"Instituto Gulbenkian de Ci\u00eancia Oeiras Portugal"}]},{"given":"Isabel","family":"Gordo","sequence":"additional","affiliation":[{"name":"Instituto Gulbenkian de Ci\u00eancia Oeiras Portugal"}]}],"member":"311","published-online":{"date-parts":[[2023,6,23]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41579\u2010021\u201000534\u20107"},{"key":"e_1_2_6_3_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3000102"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2021.02.052"},{"key":"e_1_2_6_5_1","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2021.0243"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41579\u2010020\u20100368\u20101"},{"key":"e_1_2_6_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2021.110239"},{"key":"e_1_2_6_8_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3000617"},{"key":"e_1_2_6_9_1","doi-asserted-by":"crossref","unstructured":"Tomanek I. &Guet C. 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