{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T08:20:04Z","timestamp":1790842804804,"version":"4.1.0"},"reference-count":88,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2021,11,23]],"date-time":"2021-11-23T00:00:00Z","timestamp":1637625600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 HD083040"],"award-info":[{"award-number":["R01 HD083040"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 AI094586"],"award-info":[{"award-number":["R01 AI094586"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The interaction between gut bacterial and viral microbiota is thought to be important in human health. While fluctuations in female genital tract (FGT) bacterial microbiota similarly determine sexual health, little is known about the presence, persistence, and function of vaginal bacteriophages. We conducted shotgun metagenome sequencing of cervicovaginal samples from South African adolescents collected longitudinally, who received no antibiotics. We annotated viral reads and circular bacteriophages, identified CRISPR loci and putative prophages, and assessed their diversity, persistence, and associations with bacterial microbiota composition. Siphoviridae was the most prevalent bacteriophage family, followed by Myoviridae, Podoviridae, Herelleviridae, and Inoviridae. Full-length siphoviruses targeting bacterial vaginosis (BV)-associated bacteria were identified, suggesting their presence in vivo. CRISPR loci and prophage-like elements were common, and genomic analysis suggested higher diversity among Gardnerella than Lactobacillus prophages. We found that some prophages were highly persistent within participants, and identical prophages were present in cervicovaginal secretions of multiple participants, suggesting that prophages, and thus bacterial strains, are shared between adolescents. The number of CRISPR loci and prophages were associated with vaginal microbiota stability and absence of BV. Our analysis suggests that (pro)phages are common in the FGT and vaginal bacteria and (pro)phages may interact.<\/jats:p>","DOI":"10.3390\/v13122341","type":"journal-article","created":{"date-parts":[[2021,12,1]],"date-time":"2021-12-01T03:12:56Z","timestamp":1638328376000},"page":"2341","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3658-8638","authenticated-orcid":false,"given":"Anna-Ursula","family":"Happel","sequence":"first","affiliation":[{"name":"Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3439-3992","authenticated-orcid":false,"given":"Christina","family":"Balle","sequence":"additional","affiliation":[{"name":"Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3174-9036","authenticated-orcid":false,"given":"Brandon S.","family":"Maust","sequence":"additional","affiliation":[{"name":"Seattle Children\u2019s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA"},{"name":"Department of Pediatrics, University of Washington School of Medicine, 1959 NE Pacific St., Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iyaloo N.","family":"Konstantinus","sequence":"additional","affiliation":[{"name":"Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa"},{"name":"Namibia Institute of Pathology, Hosea Kutako, Windhoek 10005, Namibia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine","family":"Gill","sequence":"additional","affiliation":[{"name":"Desmond Tutu HIV Centre, University of Cape Town, Anzio Road, Cape Town 7925, South Africa"},{"name":"NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda-Gail","family":"Bekker","sequence":"additional","affiliation":[{"name":"Desmond Tutu HIV Centre, University of Cape Town, Anzio Road, Cape Town 7925, South Africa"},{"name":"NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8234-1308","authenticated-orcid":false,"given":"R\u00e9my","family":"Froissart","sequence":"additional","affiliation":[{"name":"CNRS, IRD, Universit\u00e9 Montpellier, UMR 5290, MIVEGEC, 34394 Montpellier, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jo-Ann","family":"Passmore","sequence":"additional","affiliation":[{"name":"Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa"},{"name":"Desmond Tutu HIV Centre, University of Cape Town, Anzio Road, Cape Town 7925, South Africa"},{"name":"NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa"},{"name":"National Health Laboratory Service, Anzio Road, Cape Town 7925, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ulas","family":"Karaoz","sequence":"additional","affiliation":[{"name":"Earth and Environmental Science, Lawrence Berkeley National Laboratories, 1 Cyclotron Rd., Berkeley, CA 94720, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4111-2415","authenticated-orcid":false,"given":"Arvind","family":"Varsani","sequence":"additional","affiliation":[{"name":"The Biodesign Center of Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA"},{"name":"Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0745-6073","authenticated-orcid":false,"given":"Heather","family":"Jaspan","sequence":"additional","affiliation":[{"name":"Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa"},{"name":"Seattle Children\u2019s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA"},{"name":"Department of Pediatrics, University of Washington School of Medicine, 1959 NE Pacific St., Seattle, WA 98195, USA"},{"name":"Department of Global Health, University of Washington School of Public Health, 1510 San Juan Road NE, Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,11,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1038\/nrmicro2315","article-title":"Bacteriophage resistance mechanisms","volume":"8","author":"Labrie","year":"2010","journal-title":"Nat. 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