{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T12:10:26Z","timestamp":1768479026750,"version":"3.49.0"},"posted":{"date-parts":[[2018,8,7]]},"group-title":"Evolutionary Biology","reference-count":37,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2018,8,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Bacteria evolve by mutation accumulation in laboratory experiments, but the tempo and mode of evolution in natural environments are largely unknown. Here we show, by experimental evolution of\n                  <jats:italic>E. coli<\/jats:italic>\n                  in the mouse gut, that the ecology of the gut controls bacterial evolution. If a resident\n                  <jats:italic>E. coli<\/jats:italic>\n                  strain is present in the gut, an invading strain evolves by rapid horizontal gene transfer; this mode precedes and outweighs evolution by point mutations. An epidemic infection by two phages drives gene uptake and produces multiple co-existing lineages of phage-carrying (lysogenic) bacteria. A minimal dynamical model explains the temporal pattern of phage epidemics and their complex evolutionary outcome as generic effects of phage-mediated selection. We conclude that phages are an important eco-evolutionary driving force \u2013 they accelerate evolution and promote genetic diversity of bacteria.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>One Sentence Summary<\/jats:title>\n                  <jats:p>Bacteriophages drive rapid evolution in the gut.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/384875","type":"posted-content","created":{"date-parts":[[2018,8,7]],"date-time":"2018-08-07T18:45:16Z","timestamp":1533667516000},"source":"Crossref","is-referenced-by-count":4,"title":["Sex overrides mutation in\n                  <i>Escherichia coli<\/i>\n                  colonizing the gut"],"prefix":"10.64898","author":[{"given":"N.","family":"Fraz\u00e3o","sequence":"first","affiliation":[]},{"given":"A.","family":"Sousa","sequence":"additional","affiliation":[]},{"given":"M.","family":"L\u00e4ssig","sequence":"additional","affiliation":[]},{"given":"I.","family":"Gordo","sequence":"additional","affiliation":[]}],"member":"54368","reference":[{"key":"2019072203161474000_384875v1.1","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-016-0307-y"},{"key":"2019072203161474000_384875v1.2","doi-asserted-by":"publisher","DOI":"10.3748\/wjg.v21.i29.8787"},{"key":"2019072203161474000_384875v1.3","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1016\/j.mib.2017.05.007","article-title":"Evolution of commensal bacteria in the intestinal tract of mice","volume":"38","year":"2017","journal-title":"Curr. Opin. Microbiol."},{"key":"2019072203161474000_384875v1.4","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2006.08.024"},{"key":"2019072203161474000_384875v1.5","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3962"},{"key":"2019072203161474000_384875v1.6","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1501724112"},{"key":"2019072203161474000_384875v1.7","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.73.12.8039-8049.2005"},{"key":"2019072203161474000_384875v1.8","doi-asserted-by":"publisher","DOI":"10.1111\/mec.13851"},{"key":"2019072203161474000_384875v1.9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004182"},{"key":"2019072203161474000_384875v1.10","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2015.02.049"},{"key":"2019072203161474000_384875v1.11","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msx221"},{"key":"2019072203161474000_384875v1.12","doi-asserted-by":"publisher","DOI":"10.1038\/1841079b0"},{"key":"2019072203161474000_384875v1.13","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaf8451"},{"key":"2019072203161474000_384875v1.14","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2016.51"},{"key":"2019072203161474000_384875v1.15","first-page":"98","volume-title":"Coevolution","volume":"Chapter 5","year":"1983"},{"key":"2019072203161474000_384875v1.16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1005861"},{"key":"2019072203161474000_384875v1.17","doi-asserted-by":"crossref","first-page":"16251","DOI":"10.1038\/nmicrobiol.2016.251","article-title":"Prophage-mediated defense against viral attack and viral counter-defense","volume":"2","year":"2017","journal-title":"Nat. Microbiol."},{"key":"2019072203161474000_384875v1.18","first-page":"1199","article-title":"Selfish and spiteful behaviour through parasites and pathogens","volume":"9","year":"2007","journal-title":"Evol Ecol Res"},{"key":"2019072203161474000_384875v1.19","doi-asserted-by":"publisher","DOI":"10.1038\/nature07921"},{"key":"2019072203161474000_384875v1.20","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1305923110"},{"key":"2019072203161474000_384875v1.21","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1111\/j.1365-2672.1982.tb04730.x","article-title":"Observations on the in vivo and in vitro competition between strains of Escherichia coli isolated from the human gut","volume":"53","year":"1982","journal-title":"J. Appl. Bacteriol."},{"key":"2019072203161474000_384875v1.22","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01468-12"},{"key":"2019072203161474000_384875v1.23","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.95.6.3140"},{"key":"2019072203161474000_384875v1.24","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/19.24.6823"},{"key":"2019072203161474000_384875v1.25","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00009-15."},{"key":"2019072203161474000_384875v1.26","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.f.303"},{"key":"2019072203161474000_384875v1.27","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.545"},{"key":"2019072203161474000_384875v1.28","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2011.139"},{"key":"2019072203161474000_384875v1.29","doi-asserted-by":"publisher","DOI":"10.1145\/584091.584093"},{"key":"2019072203161474000_384875v1.30","unstructured":"K. Wilson , in Current Protocols in Molecular Biology, F. M. Ausubel et al ., Eds. (John Wiley & Sons, Inc., Hoboken, NJ, USA, 2001; http:\/\/doi.wiley.com\/10.1002\/0471142727.mb0204s56)."},{"key":"2019072203161474000_384875v1.31","doi-asserted-by":"publisher","DOI":"10.1038\/nature08480"},{"key":"2019072203161474000_384875v1.32","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1754"},{"key":"2019072203161474000_384875v1.33","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1990.9999"},{"key":"2019072203161474000_384875v1.34","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw387"},{"key":"2019072203161474000_384875v1.35","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr039"},{"key":"2019072203161474000_384875v1.36","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3869"},{"key":"2019072203161474000_384875v1.37","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1111\/j.1442-9993.1993.tb00438.x","article-title":"Non-parametric multivariate analyses of changes in community structure","volume":"18","year":"1993","journal-title":"Austral Ecol."}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/384875","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,14]],"date-time":"2026-01-14T22:51:08Z","timestamp":1768431068000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/384875"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,8,7]]},"references-count":37,"URL":"https:\/\/doi.org\/10.1101\/384875","relation":{"is-preprint-of":[{"id-type":"doi","id":"10.1073\/pnas.1906958116","asserted-by":"subject"}]},"subject":[],"published":{"date-parts":[[2018,8,7]]},"subtype":"preprint"}}