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Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2018,2,13]]},"abstract":"<jats:p>\n                    The mature human gut microbiota is established during the first years of life, and altered intestinal microbiomes have been associated with several human health disorders.\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    usually represents less than 1% of the human intestinal microbiome, whereas in cystic fibrosis (CF), greater than 50% relative abundance is common and correlates with intestinal inflammation and fecal fat malabsorption. Despite the proliferation of\n                    <jats:italic>E. coli<\/jats:italic>\n                    and other Proteobacteria in conditions involving chronic gastrointestinal tract inflammation, little is known about adaptation of specific characteristics associated with microbiota clonal expansion. We show that\n                    <jats:italic>E. coli<\/jats:italic>\n                    isolated from fecal samples of young children with CF has adapted to growth on glycerol, a major component of fecal fat.\n                    <jats:italic>E. coli<\/jats:italic>\n                    isolates from different CF patients demonstrate an increased growth rate in the presence of glycerol compared with\n                    <jats:italic>E. coli<\/jats:italic>\n                    from healthy controls, and unrelated CF\n                    <jats:italic>E. coli<\/jats:italic>\n                    strains have independently acquired this growth trait. Furthermore, CF and control\n                    <jats:italic>E. coli<\/jats:italic>\n                    isolates have differential gene expression when grown in minimal media with glycerol as the sole carbon source. While CF isolates display a growth-promoting transcriptional profile, control isolates engage stress and stationary-phase programs, which likely results in slower growth rates. Our results indicate that there is selection of unique characteristics within the microbiome of individuals with CF, which could contribute to individual disease outcomes.\n                  <\/jats:p>","DOI":"10.1073\/pnas.1714373115","type":"journal-article","created":{"date-parts":[[2018,1,29]],"date-time":"2018-01-29T15:15:57Z","timestamp":1517238957000},"page":"1605-1610","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":55,"title":["Adaptation of commensal proliferating\n                    <i>Escherichia coli<\/i>\n                    to the intestinal tract of young children with cystic fibrosis"],"prefix":"10.1073","volume":"115","author":[{"given":"Susana","family":"Matamouros","sequence":"first","affiliation":[{"name":"Department of Microbiology, University of Washington, Seattle, WA 98195;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hillary S.","family":"Hayden","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Washington, Seattle, WA 98195;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyle R.","family":"Hager","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Washington, Seattle, WA 98195;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mitchell J.","family":"Brittnacher","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Washington, Seattle, WA 98195;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristina","family":"Lachance","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Washington, Seattle, WA 98195;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eli J.","family":"Weiss","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Washington, Seattle, WA 98195;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher E.","family":"Pope","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Washington, Seattle, WA 98195;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne-Flore","family":"Imhaus","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Washington, Seattle, WA 98195;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Colin P.","family":"McNally","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle, WA 98195;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elhanan","family":"Borenstein","sequence":"additional","affiliation":[{"name":"Department of Genome Sciences, University of Washington, Seattle, WA 98195;"},{"name":"Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195;"},{"name":"Santa Fe Institute, Santa Fe, NM 87501;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucas R.","family":"Hoffman","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Washington, Seattle, WA 98195;"},{"name":"Department of Pediatrics, University of Washington, Seattle, WA 98195;"},{"name":"Seattle Children\u2019s Hospital, Seattle, WA 98105;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel I.","family":"Miller","sequence":"additional","affiliation":[{"name":"Department of Microbiology, University of Washington, Seattle, WA 98195;"},{"name":"Department of Genome Sciences, University of Washington, Seattle, WA 98195;"},{"name":"Department of Medicine, University of Washington, Seattle, WA 98195"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2018,1,29]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1053\/j.gastro.2008.10.080","article-title":"Microbes in gastrointestinal health and disease","volume":"136","author":"Neish AS","year":"2009","unstructured":"AS Neish, Microbes in gastrointestinal health and disease. 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