{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:46:21Z","timestamp":1790729181901,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.ppat.1013836","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,1,14]],"date-time":"2026-01-14T00:00:00Z","timestamp":1768348800000}}],"reference-count":89,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2026,1,2]],"date-time":"2026-01-02T00:00:00Z","timestamp":1767312000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["R01DK124317"],"award-info":[{"award-number":["R01DK124317"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["P20GM103474"],"award-info":[{"award-number":["P20GM103474"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["366502"],"award-info":[{"award-number":["366502"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","award":["UM1TR004409"],"award-info":[{"award-number":["UM1TR004409"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","award":["K12TR004413"],"award-info":[{"award-number":["K12TR004413"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100002799","name":"Intermountain Healthcare","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100002799","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    Prophages are prevalent features of bacterial genomes that can reduce susceptibility to infection by competing phages, yet the mechanisms involved are often elusive. Here, we identify a small RNA (svsR) encoded by the lambdoid prophage NC-SV in adherent-invasive\n                    <jats:italic>\n                      <jats:italic>Escherichia coli<\/jats:italic>\n                    <\/jats:italic>\n                    strain NC101 that limits infection by virulent coliphages. Comparative genomics revealed that NC-SV\u2013like prophages and\n                    <jats:italic>\n                      <jats:italic>svsR<\/jats:italic>\n                    <\/jats:italic>\n                    homologs are broadly conserved across Enterobacteriaceae. Transcriptomic analyses show that svsR represses maltodextrin transport genes, including\n                    <jats:italic>\n                      <jats:italic>lamB<\/jats:italic>\n                    <\/jats:italic>\n                    , which encodes the outer membrane maltoporin LamB, a known receptor for numerous coliphages. Deletion of the\n                    <jats:italic>\n                      <jats:italic>lamB<\/jats:italic>\n                    <\/jats:italic>\n                    gene reveals that while LamB is not required for replication of the virulent phages tested, it contributes to plaque expansion, indicating a role in phage spread but not as an essential receptor. Nutrient supplementation experiments further linked maltodextrin and glucose availability to changes in plaque expansion and phage adsorption.\n                    <jats:italic>\n                      <jats:italic>In vivo,<\/jats:italic>\n                    <\/jats:italic>\n                    we compared wild-type NC101 and a prophage-deletion strain (NC101\n                    <jats:sup>\u2206NC-SV<\/jats:sup>\n                    ) in mice to assess the impact of NC-SV on lytic phage susceptibility. Although intestinal\n                    <jats:italic>\n                      <jats:italic>E. coli<\/jats:italic>\n                    <\/jats:italic>\n                    densities remained stable across groups, animals colonized with NC101 exhibited markedly reduced phage burdens in both the intestinal lumen and mucosa compared to mice colonized with NC101\n                    <jats:sup>\u2206NC-SV<\/jats:sup>\n                    . This reduced phage pressure was associated with increased dissemination of\n                    <jats:italic>\n                      <jats:italic>E. coli<\/jats:italic>\n                    <\/jats:italic>\n                    to extraintestinal tissues, including the spleen and liver. Together, these findings highlight a nutrient-responsive, prophage-encoded mechanism that protects\n                    <jats:italic>\n                      <jats:italic>E. coli<\/jats:italic>\n                    <\/jats:italic>\n                    from phage predation and may promote bacterial persistence in and dissemination from the mammalian gut.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1013836","type":"journal-article","created":{"date-parts":[[2026,1,2]],"date-time":"2026-01-02T19:03:28Z","timestamp":1767380608000},"page":"e1013836","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["A prophage-encoded sRNA limits phage infection of adherent-invasive E. coli"],"prefix":"10.1371","volume":"22","author":[{"given":"Nicole L.","family":"Pershing","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert S.","family":"Brzozowski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amelia K.","family":"Schmidt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dominick R.","family":"Faith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex C.","family":"Joyce","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lizett Ortiz","family":"de Ora","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John D.","family":"Kominsky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annika","family":"Dankwardt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Maciver","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rickesha","family":"Bell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William S.","family":"Henriques","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shelby E.","family":"Andersen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Blake","family":"Wiedenheft","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sherwood R.","family":"Casjens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Breck A.","family":"Duerkop","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"June L.","family":"Round","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7123-3037","authenticated-orcid":true,"given":"Patrick R.","family":"Secor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,1,2]]},"reference":[{"issue":"11","key":"ppat.1013836.ref001","doi-asserted-by":"crossref","first-page":"2726","DOI":"10.1128\/JB.00787-10","article-title":"Prophage-stimulated toxin production in Clostridium difficile NAP1\/027 lysogens","volume":"193","author":"O Sekulovic","year":"2011","journal-title":"J 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