{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T12:05:42Z","timestamp":1788869142970,"version":"build-2803163510"},"reference-count":91,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2022,1,20]],"date-time":"2022-01-20T00:00:00Z","timestamp":1642636800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001713","name":"European &amp; Developing Countries Clinical Trials Partnership","doi-asserted-by":"publisher","award":["SP\u00b72011\u00b741304\u00b7038"],"award-info":[{"award-number":["SP\u00b72011\u00b741304\u00b7038"]}],"id":[{"id":"10.13039\/501100001713","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001713","name":"European &amp; Developing Countries Clinical Trials Partnership","doi-asserted-by":"publisher","award":["TMA2020CDF-3192-VaViBa"],"award-info":[{"award-number":["TMA2020CDF-3192-VaViBa"]}],"id":[{"id":"10.13039\/501100001713","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001323","name":"Poliomyelitis Research Foundation","doi-asserted-by":"publisher","award":["15\/23"],"award-info":[{"award-number":["15\/23"]}],"id":[{"id":"10.13039\/501100001323","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001323","name":"Poliomyelitis Research Foundation","doi-asserted-by":"publisher","award":["15\/64"],"award-info":[{"award-number":["15\/64"]}],"id":[{"id":"10.13039\/501100001323","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001321","name":"National Research Foundation","doi-asserted-by":"publisher","award":["UID 116674"],"award-info":[{"award-number":["UID 116674"]}],"id":[{"id":"10.13039\/501100001321","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>While live biotherapeutics offer a promising approach to optimizing vaginal microbiota, the presence of functional prophages within introduced Lactobacillaceae strains could impact their safety and efficacy. We evaluated the presence of prophages in 895 publicly available Lactobacillaceae genomes using Phaster, Phigaro, Phispy, Prophet and Virsorter. Prophages were identified according to stringent (detected by \u22654 methods) or lenient criteria (detected by \u22652 methods), both with &gt;80% reciprocal sequence overlap. The stringent approach identified 448 prophages within 359 genomes, with 40.1% genomes harbouring at least one prophage, while the lenient approach identified 1671 prophages within 83.7% of the genomes. To confirm our in silico estimates in vitro, we tested for inducible prophages in 57 vaginally-derived and commercial Lactobacillaceae isolates and found inducible prophages in 61.4% of the isolates. We characterised the in silico predicted prophages based on weighted gene repertoire relatedness and found that most belonged to the Siphoviridae or Myoviridae families. ResFam and eggNOG identified four potential antimicrobial resistance genes within the predicted prophages. Our results suggest that while Lactobacillaceae prophages seldomly carry clinically concerning genes and thus unlikely a pose a direct risk to human vaginal microbiomes, their high prevalence warrants the characterisation of Lactobacillaceae prophages in live biotherapeutics.<\/jats:p>","DOI":"10.3390\/microorganisms10020214","type":"journal-article","created":{"date-parts":[[2022,1,20]],"date-time":"2022-01-20T22:51:06Z","timestamp":1642719066000},"page":"214","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["In Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Health"],"prefix":"10.3390","volume":"10","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"}]},{"given":"Brian R.","family":"Kullin","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"}]},{"given":"Hoyam","family":"Gamieldien","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\/0000-0002-0745-6073","authenticated-orcid":false,"given":"Heather B.","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 and Global Health, University of Washington, 1410 NE Campus Parkway NE, Seattle, WA 98195, 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"}]},{"given":"Darren","family":"Martin","sequence":"additional","affiliation":[{"name":"Division of Computational Biology, 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"}]},{"given":"Jo-Ann S.","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":"NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa"},{"name":"National Health Laboratory Service, Cape Town 7925, 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"}]}],"member":"1968","published-online":{"date-parts":[[2022,1,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1089\/aid.2018.0304","article-title":"The Evolving Facets of Bacterial Vaginosis: Implications for HIV Transmission","volume":"35","author":"McKinnon","year":"2019","journal-title":"AIDS Res. 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