{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T12:14:25Z","timestamp":1785413665138,"version":"3.56.0"},"reference-count":85,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T00:00:00Z","timestamp":1777507200000},"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":"crossref","award":["NIH R01 HD083040"],"award-info":[{"award-number":["NIH R01 HD083040"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01 HD106821"],"award-info":[{"award-number":["R01 HD106821"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"award":["NIH R01 HD083040"],"award-info":[{"award-number":["NIH R01 HD083040"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R01 HD106821"],"award-info":[{"award-number":["R01 HD106821"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Gates Foundation","award":["INV-048980"],"award-info":[{"award-number":["INV-048980"]}]},{"award":["INV-048980"],"award-info":[{"award-number":["INV-048980"]}],"id":[{"id":"https:\/\/ror.org\/0456r8d26","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001713","name":"European Union","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"}]},{"award":["TMA2020CDF-3192-VaViBa"],"award-info":[{"award-number":["TMA2020CDF-3192-VaViBa"]}],"id":[{"id":"https:\/\/ror.org\/019w4f821","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001323","name":"Poliomyelitis Research Foundation","doi-asserted-by":"publisher","award":["22\/109"],"award-info":[{"award-number":["22\/109"]}],"id":[{"id":"10.13039\/501100001323","id-type":"DOI","asserted-by":"publisher"}]},{"award":["22\/109"],"award-info":[{"award-number":["22\/109"]}],"id":[{"id":"https:\/\/ror.org\/02d540t02","id-type":"ROR","asserted-by":"publisher"}]},{"name":"UCT Incoming International Students Scholarship"},{"name":"Margaret McNamara Education Grant"},{"name":"Mawazo Institute"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Lactobacillus crispatus is widely associated with optimal sexual and reproductive health outcomes. While L. crispatus genomes commonly harbor prophages, little is known about their genomic diversity and potential inducibility by clinically relevant compounds. We induced and characterized four bacteriophages from four L. crispatus strains isolated from vaginal secretions of South African adolescents. Sequenced viral DNA from induced phages was assembled, and their respective genomes were annotated and compared to bacteriophage reference genomes. All the phage genomes range in size from 42.9 to 48.3 kbp. Of the four phages, UC101 and UC164 shared &lt;90% pairwise intergenomic similarity to reference phages, suggesting that they represent new species. To explore factors potentially associated with prophage activation, L. crispatus strains were exposed to physiological concentrations of copper ions and tenofovir, selected based on their common use by women in Africa and reported associations with altered vaginal bacterial community composition. The presence of phage-like particles following exposure to copper ions (2.0 \u00d7 10\u22126 M\u20133.0 \u00d7 10\u22126 M) and tenofovir (500 ng\/mL) was observed by transmission electron microscopy, suggesting possible prophage activation under these conditions. This study provides new insights into the genomic diversity of inducible L. crispatus phages and presents hypothesis-generating evidence regarding their potential inducibility using copper ions and tenofovir.<\/jats:p>","DOI":"10.3390\/v18050519","type":"journal-article","created":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T10:47:28Z","timestamp":1777546048000},"page":"519","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic Diversity of Vaginal Lactobacillus crispatus Prophages from South African Women"],"prefix":"10.3390","volume":"18","author":[{"given":"Adijat Ozohu","family":"Jimoh","sequence":"first","affiliation":[{"name":"Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa"},{"name":"Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa"},{"name":"Genetics, Genomics, and Bioinformatics Department, National Biotechnology Research and Development Agency, Abuja 900107, Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6166-6269","authenticated-orcid":false,"given":"Anika","family":"Chicken","sequence":"additional","affiliation":[{"name":"Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa"},{"name":"Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town 7925, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3174-9036","authenticated-orcid":false,"given":"Brandon","family":"Maust","sequence":"additional","affiliation":[{"name":"Center for Global Infectious Disease Research, Seattle Children\u2019s Research Institute, Seattle, WA 98109, USA"},{"name":"Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Colin","family":"Feng","sequence":"additional","affiliation":[{"name":"Center for Global Infectious Disease Research, Seattle Children\u2019s Research Institute, Seattle, WA 98109, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seth","family":"Rakoff-Nahoum","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Boston Children\u2019s Hospital and Harvard Medical School, Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jo-Ann S.","family":"Passmore","sequence":"additional","affiliation":[{"name":"Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa"},{"name":"National Health Laboratory Services, Cape Town 7925, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5460-1977","authenticated-orcid":false,"given":"Brian R.","family":"Kullin","sequence":"additional","affiliation":[{"name":"Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7037-9242","authenticated-orcid":false,"given":"Simona","family":"Kraberger","sequence":"additional","affiliation":[{"name":"The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fatima Aysha","family":"Hussain","sequence":"additional","affiliation":[{"name":"Department of Biology, Tufts University, Medford, MA 02155, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heather B.","family":"Jaspan","sequence":"additional","affiliation":[{"name":"Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa"},{"name":"Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa"},{"name":"Center for Global Infectious Disease Research, Seattle Children\u2019s Research Institute, Seattle, WA 98109, USA"},{"name":"Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA"},{"name":"Department of Global Health, University of Washington, Seattle, WA 3980, 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 for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA"},{"name":"Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3658-8638","authenticated-orcid":false,"given":"Anna-Ursula","family":"Happel","sequence":"additional","affiliation":[{"name":"Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa"},{"name":"Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,4,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/s40168-016-0223-9","article-title":"The Interaction between Vaginal Microbiota, Cervical Length, and Vaginal Progesterone Treatment for Preterm Birth Risk","volume":"5","author":"Kindinger","year":"2017","journal-title":"Microbiome"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Brown, R.G., Marchesi, J.R., Lee, Y.S., Smith, A., Lehne, B., Kindinger, L.M., Terzidou, V., Holmes, E., Nicholson, J.K., and Bennett, P.R. (2018). Vaginal Dysbiosis Increases Risk of Preterm Fetal Membrane Rupture, Neonatal Sepsis and Is Exacerbated by Erythromycin. BMC Med., 16.","DOI":"10.1186\/s12916-017-0999-x"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"29024","DOI":"10.1038\/srep29024","article-title":"Lactobacillus crispatus Inhibits the Infectivity of Chlamydia trachomatis Elementary Bodies, In Vitro Study","volume":"6","author":"Nardini","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Petrova, M.I., Lievens, E., Malik, S., Imholz, N., and Lebeer, S. (2015). Lactobacillus Species as Biomarkers and Agents That Can Promote Various Aspects of Vaginal Health. Front. Physiol., 6.","DOI":"10.3389\/fphys.2015.00081"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1113\/JP271694","article-title":"The Vaginal Microbiota, Host Defence and Reproductive Physiology","volume":"595","author":"Smith","year":"2017","journal-title":"J. Physiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1186\/s40168-025-02066-1","article-title":"Exploring the Female Genital Tract Mycobiome in Young South African Women Using Metaproteomics","volume":"13","author":"Gangiah","year":"2025","journal-title":"Microbiome"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1136\/sextrans-2024-056260","article-title":"Differences in HIV Risk Factors between South African Adolescents and Adult Women and Their Association with Sexually Transmitted Infections","volume":"101","author":"Mkhize","year":"2025","journal-title":"Sex. Transm. Infect."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.1177\/0956462415616038","article-title":"Prevalent Bacterial Vaginosis Infection\u2014A Risk Factor for Incident Sexually Transmitted Infections in Women in Durban, South Africa","volume":"27","author":"Abbai","year":"2016","journal-title":"Int. J. STD AIDS"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1012","DOI":"10.1038\/s41591-019-0450-2","article-title":"The Vaginal Microbiome and Preterm Birth","volume":"25","author":"Fettweis","year":"2019","journal-title":"Nat. Med."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1136\/sextrans-2015-052285","article-title":"Identification of Novel Microbes Associated with Pelvic Inflammatory Disease and Infertility","volume":"92","author":"Haggerty","year":"2016","journal-title":"Sex. Transm. Infect."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"2682","DOI":"10.1007\/s10995-015-1790-2","article-title":"First Trimester Levels of BV-Associated Bacteria and Risk of Miscarriage Among Women Early in Pregnancy","volume":"19","author":"Nelson","year":"2015","journal-title":"Matern. Child Health J."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"S137","DOI":"10.1093\/infdis\/jiab103","article-title":"Bacterial Vaginosis and Behavioral Factors Associated With Incident Pelvic Inflammatory Disease in the Longitudinal Study of Vaginal Flora","volume":"224","author":"Turpin","year":"2021","journal-title":"J. Infect. Dis."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Happel, A.-U., Varsani, A., Balle, C., Passmore, J.-A., and Jaspan, H. (2020). The Vaginal Virome\u2014Balancing Female Genital Tract Bacteriome, Mucosal Immunity, and Sexual and Reproductive Health Outcomes?. Viruses, 12.","DOI":"10.3390\/v12080832"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1700112","DOI":"10.1002\/bies.201700112","article-title":"Ecological and Evolutionary Benefits of Temperate Phage: What Does or Doesn\u2019t Kill You Makes You Stronger","volume":"39","author":"Harrison","year":"2017","journal-title":"BioEssays"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Laumay, F., Corvaglia, A.-R., Diene, S.M., Girard, M., Oechslin, F., van der Mee-Marquet, N., Entenza, J.M., and Fran\u00e7ois, P. (2019). Temperate Prophages Increase Bacterial Adhesin Expression and Virulence in an Experimental Model of Endocarditis Due to Staphylococcus aureus From the CC398 Lineage. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.00742"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1146\/annurev-virology-010421-053015","article-title":"Integrating Viral Metagenomics into an Ecological Framework","volume":"8","author":"Sommers","year":"2021","journal-title":"Annu. Rev. Virol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Happel, A.-U., Balle, C., Maust, B.S., Konstantinus, I.N., Gill, K., Bekker, L.-G., Froissart, R., Passmore, J.-A., Karaoz, U., and Varsani, A. (2021). Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents. Viruses, 13.","DOI":"10.3390\/v13122341"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Happel, A.-U., Kullin, B.R., Gamieldien, H., Jaspan, H.B., Varsani, A., Martin, D., Passmore, J.-A.S., and Froissart, R. (2022). In Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Health. Microorganisms, 10.","DOI":"10.3390\/microorganisms10020214"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"90","DOI":"10.3103\/S0891416820020093","article-title":"Prophage Sequences in Genomes of Vaginal Lactobacteria","volume":"35","author":"Starikova","year":"2020","journal-title":"Mol. Genet. Microbiol. Virol."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Wiafe-Kwakye, C.S., Fournier, A., Maurais, H., Southworth, K.J., Molloy, S.D., and Neely, M.N. (2024). Comparative Genomic Analysis of Prophages in Human Vaginal Isolates of Streptococcus agalactiae. Pathogens, 13.","DOI":"10.3390\/pathogens13080610"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"lqaa001","DOI":"10.1093\/nargab\/lqaa001","article-title":"Host and Body Site-Specific Adaptation of Lactobacillus crispatus Genomes","volume":"2","author":"Pan","year":"2020","journal-title":"NAR Genom. Bioinform."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1099\/jmm.0.024463-0","article-title":"Identification of Predominant Culturable Vaginal Lactobacillus Species and Associated Bacteriophages from Women with and without Vaginal Discharge Syndrome in South Africa","volume":"60","author":"Damelin","year":"2011","journal-title":"J. Med. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1017\/S0022029923000274","article-title":"Detection of Lytic Phage Infecting Flavour-Producing Strain of Lacticaseibacillus paracasei in the Dairy Effluents of Kerala","volume":"90","author":"Chandran","year":"2023","journal-title":"J. Dairy Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"104203","DOI":"10.1016\/j.resmic.2024.104203","article-title":"Whole Genome Analysis, Thermal and UV-Tolerance of Lactococcus Phage BIM BV-114 Isolated from Cheese Brine","volume":"175","author":"Herasimovich","year":"2024","journal-title":"Res. Microbiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.ijfoodmicro.2019.05.008","article-title":"Virulence of Leuconostoc Phages: Influence of Stress Conditions Associated to Dairy Processes on Their Host-Phage Interactions","volume":"303","author":"Quiberoni","year":"2019","journal-title":"Int. J. Food Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Ali, M., Folz, R., and Farron, M. (2019). Expanding Choice and Access in Contraception: An Assessment of Intrauterine Contraception Policies in Low and Middle-Income Countries. BMC Public Health, 19.","DOI":"10.1186\/s12889-019-8080-7"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.contraception.2021.11.002","article-title":"Contraceptive Method Preference and Reasons for Contraceptive Discontinuation among Women Randomized to Intramuscular Depot Medroxyprogesterone Acetate, a Copper Intrauterine Device or a Levonorgestrel Implant: Findings from Durban, South Africa","volume":"108","author":"Beesham","year":"2022","journal-title":"Contraception"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/s41467-023-36002-4","article-title":"Copper Intrauterine Device Increases Vaginal Concentrations of Inflammatory Anaerobes and Depletes Lactobacilli Compared to Hormonal Options in a Randomized Trial","volume":"14","author":"Brown","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1093\/cid\/ciaa703","article-title":"Elevated Risk of Bacterial Vaginosis Among Users of the Copper Intrauterine Device: A Prospective Longitudinal Cohort Study","volume":"73","author":"Peebles","year":"2021","journal-title":"Clin. Infect. Dis."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"110936","DOI":"10.1016\/j.contraception.2025.110936","article-title":"Effect of Contraceptive Methods on the Vaginal Microbiome and Host Immune Factors","volume":"148","author":"Serrano","year":"2025","journal-title":"Contraception"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"3966","DOI":"10.4102\/PHCFM.v16i1.3966","article-title":"How Do South African Policies Address Provision of Contraception among Adolescents?","volume":"16","author":"Ketye","year":"2024","journal-title":"Afr. J. Prim. Health Care Fam. Med."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1126\/science.aai9383","article-title":"Vaginal Bacteria Modify HIV Tenofovir Microbicide Efficacy in African Women","volume":"356","author":"Klatt","year":"2017","journal-title":"Science"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/S1383-5718(00)00003-6","article-title":"Induction of Vaginal Lactobacillus Phages by the Cigarette Smoke Chemical Benzo[a]Pyrene Diol Epoxide","volume":"466","author":"Pavlova","year":"2000","journal-title":"Mutat. Res.\/Genet. Toxicol. Environ. Mutagen."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"e25626","DOI":"10.1002\/jia2.25626","article-title":"An Open-Label, Randomized Crossover Study to Evaluate the Acceptability and Preference for Contraceptive Options in Female Adolescents, 15 to 19 Years of Age in Cape Town, as a Proxy for HIV Prevention Methods (UChoose)","volume":"23","author":"Gill","year":"2020","journal-title":"J. Int. AIDS Soc."},{"key":"ref_35","unstructured":"Chicken, A. (2024). Characterising Vaginal Lactobacillus Strains from Young South African Women with Persistently Optimal Vaginal Microbiota\u2014Developing the Framework for an African Vaginal Probiotic Product Development Platform for Reproductive Health. [Master\u2019s Thesis, University of Cape Town]."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1128\/jb.173.2.697-703.1991","article-title":"16S Ribosomal DNA Amplification for Phylogenetic Study","volume":"173","author":"Weisburg","year":"1991","journal-title":"J. Bacteriol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"6955","DOI":"10.1073\/pnas.82.20.6955","article-title":"Rapid Determination of 16S Ribosomal RNA Sequences for Phylogenetic Analyses","volume":"82","author":"Lane","year":"1985","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1089\/10665270050081478","article-title":"A Greedy Algorithm for Aligning DNA Sequences","volume":"7","author":"Zhang","year":"2000","journal-title":"J. Comput. Biol."},{"key":"ref_39","unstructured":"Andrews, S. (2025, November 06). FastQC: A Quality Control Tool for High Throughput Sequence Data. Available online: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/j.virol.2018.01.002","article-title":"Classification and Evolution of Human Papillomavirus Genome Variants: Alpha-5 (HPV26, 51, 69, 82), Alpha-6 (HPV30, 53, 56, 66), Alpha-11 (HPV34, 73), Alpha-13 (HPV54) and Alpha-3 (HPV61)","volume":"516","author":"Chen","year":"2018","journal-title":"Virology"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"e102","DOI":"10.1002\/cpbi.102","article-title":"Using SPAdes De Novo Assembler","volume":"70","author":"Prjibelski","year":"2020","journal-title":"Curr. Protoc. Bioinform."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"i142","DOI":"10.1093\/bioinformatics\/bty266","article-title":"Versatile Genome Assembly Evaluation with QUAST-LG","volume":"34","author":"Mikheenko","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid Prokaryotic Genome Annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/s40168-020-00990-y","article-title":"VirSorter2: A Multi-Classifier, Expert-Guided Approach to Detect Diverse DNA and RNA Viruses","volume":"9","author":"Guo","year":"2021","journal-title":"Microbiome"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1038\/s41587-020-00774-7","article-title":"CheckV Assesses the Quality and Completeness of Metagenome-Assembled Viral Genomes","volume":"39","author":"Nayfach","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: A Better, Faster Version of the PHAST Phage Search Tool","volume":"44","author":"Arndt","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e2261","DOI":"10.7717\/peerj.2261","article-title":"Phage on Tap\u2013a Quick and Efficient Protocol for the Preparation of Bacteriophage Laboratory Stocks","volume":"4","author":"Bonilla","year":"2016","journal-title":"PeerJ"},{"key":"ref_48","unstructured":"Tumban, E. (2024). Phage DNA Extraction, Genome Assembly, and Genome Closure. Bacteriophages: Methods and Protocols, Springer."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A Flexible Trimmer for Illumina Sequence Data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.ymeth.2016.02.020","article-title":"MEGAHIT v1.0: A Fast and Scalable Metagenome Assembler Driven by Advanced Methodologies and Community Practices","volume":"102","author":"Li","year":"2016","journal-title":"Methods"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"veaa100","DOI":"10.1093\/ve\/veaa100","article-title":"Cenote-Taker 2 Democratizes Virus Discovery and Sequence Annotation","volume":"7","author":"Tisza","year":"2021","journal-title":"Virus Evol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"btac776","DOI":"10.1093\/bioinformatics\/btac776","article-title":"Pharokka: A Fast Scalable Bacteriophage Annotation Tool","volume":"39","author":"Bouras","year":"2023","journal-title":"Bioinformatics"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1093\/bib\/bbx108","article-title":"MAFFT Online Service: Multiple Sequence Alignment, Interactive Sequence Choice and Visualization","volume":"20","author":"Katoh","year":"2019","journal-title":"Brief. Bioinform."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"2379","DOI":"10.1093\/bioinformatics\/btx157","article-title":"ViPTree: The Viral Proteomic Tree Server","volume":"33","author":"Nishimura","year":"2017","journal-title":"Bioinformatics"},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Moraru, C., Varsani, A., and Kropinski, A.M. (2020). VIRIDIC-A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses. Viruses, 12.","DOI":"10.1101\/2020.07.05.188268"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"2473","DOI":"10.1093\/bioinformatics\/btab007","article-title":"Clinker & Clustermap.Js: Automatic Generation of Gene Cluster Comparison Figures","volume":"37","author":"Gilchrist","year":"2021","journal-title":"Bioinformatics"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/S0009-8981(03)00124-4","article-title":"Characterization of Copper in Uterine Fluids of Patients Who Use the Copper T-380A Intrauterine Device","volume":"332","author":"Arancibia","year":"2003","journal-title":"Clin. Chim. Acta"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1002\/ijgo.15356","article-title":"Copper Levels in Cervical Mucus of Copper Intrauterine Device Users versus Non-Users","volume":"165","author":"Han","year":"2024","journal-title":"Int. J. Gynecol. Obstet."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1097\/QAI.0000000000000607","article-title":"Genital Tenofovir Concentrations Correlate with Protection against HIV Infection in the CAPRISA 004 Trial: Importance of Adherence for Microbicide Effectiveness","volume":"69","author":"Kashuba","year":"2015","journal-title":"J. Acquir. Immune Defic. Syndr."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1097\/QAI.0000000000002884","article-title":"Genital Inflammation Is Not Associated With Decreased Vaginal Tenofovir Concentrations in Women Taking Oral PrEP","volume":"89","author":"Morris","year":"2022","journal-title":"J. Acquir. Immune Defic. Syndr."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1097\/QAI.0000000000002820","article-title":"Genital Mucosal Drug Concentrations and Anti-HIV Activity in Tenofovir-Based PrEP Products: Intravaginal Ring vs. Oral Administration","volume":"89","author":"Ouattara","year":"2022","journal-title":"J. Acquir. Immune Defic. Syndr."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1128\/CDLI.8.1.31-39.2001","article-title":"Comparative Study of Vaginal Lactobacillus Phages Isolated from Women in the United States and Turkey: Prevalence, Morphology, Host Range, and DNA Homology","volume":"8","author":"Pavlova","year":"2001","journal-title":"Clin. Diagn. Lab. Immunol."},{"key":"ref_63","first-page":"793172","article-title":"Phage Infection in Vaginal Lactobacilli: An In Vitro Study","volume":"5","author":"Pavlova","year":"1997","journal-title":"Infect. Dis. Obstet. Gynecol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1038\/s41586-025-09786-2","article-title":"Long-Read Metagenomics Reveals Phage Dynamics in the Human Gut Microbiome","volume":"649","author":"Wirbel","year":"2025","journal-title":"Nature"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"3130","DOI":"10.1128\/AEM.72.5.3130-3146.2006","article-title":"Comparative Genomics and Transcriptional Analysis of Prophages Identified in the Genomes of Lactobacillus gasseri, Lactobacillus salivarius, and Lactobacillus casei","volume":"72","author":"Ventura","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"e2023202118","DOI":"10.1073\/pnas.2023202118","article-title":"A Catalog of Tens of Thousands of Viruses from Human Metagenomes Reveals Hidden Associations with Chronic Diseases","volume":"118","author":"Tisza","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"e01922-19","DOI":"10.1128\/AEM.01922-19","article-title":"Prophages in Lactobacillus reuteri Are Associated with Fitness Trade-Offs but Can Increase Competitiveness in the Gut Ecosystem","volume":"86","author":"Oh","year":"2019","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"1516","DOI":"10.1093\/gbe\/evy106","article-title":"Phylogenomic Analysis of Lactobacillus Curvatus Reveals Two Lineages Distinguished by Genes for Fermenting Plant-Derived Carbohydrates","volume":"10","author":"Coeuret","year":"2018","journal-title":"Genome Biol. Evol."},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Bucher, M.J., and Czy\u017c, D.M. (2024). Phage against the Machine: The SIE-Ence of Superinfection Exclusion. Viruses, 16.","DOI":"10.3390\/v16091348"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"2854","DOI":"10.1038\/ismej.2016.79","article-title":"Prophages Mediate Defense against Phage Infection through Diverse Mechanisms","volume":"10","author":"Qian","year":"2016","journal-title":"ISME J."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"e02441-21","DOI":"10.1128\/mbio.02441-21","article-title":"A Filamentous Bacteriophage Protein Inhibits Type IV Pili To Prevent Superinfection of Pseudomonas aeruginosa","volume":"13","author":"Schmidt","year":"2022","journal-title":"mBio"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.virol.2006.03.001","article-title":"The Ltp Gene of Temperate Streptococcus thermophilus Phage TP-J34 Confers Superinfection Exclusion to Streptococcus thermophilus and Lactococcus lactis","volume":"350","author":"Sun","year":"2006","journal-title":"Virology"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"103913","DOI":"10.1016\/j.fm.2021.103913","article-title":"Distribution and Characterization of Prophages in Lactobacillus plantarum Derived from Kimchi","volume":"102","author":"Park","year":"2022","journal-title":"Food Microbiol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/j.virol.2003.08.019","article-title":"The Prophage Sequences of Lactobacillus plantarum Strain WCFS1","volume":"316","author":"Ventura","year":"2003","journal-title":"Virology"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"21567","DOI":"10.1038\/s41598-021-00998-w","article-title":"Distribution and Genome Structures of Temperate Phages in Acetic Acid Bacteria","volume":"11","author":"Omata","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1007\/978-1-0716-3523-0_3","article-title":"Bacteriophage Taxonomy: A Continually Evolving Discipline","volume":"Volume 2734","author":"Azeredo","year":"2024","journal-title":"Bacteriophage Therapy"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"e0114322","DOI":"10.1128\/mra.01143-22","article-title":"Genome Sequences of Anelloviruses, a Genomovirus, Microviruses, Polyomaviruses, and an Unclassified Caudovirus Identified in Vaginal Secretions from South African Adolescents","volume":"12","author":"Jimoh","year":"2023","journal-title":"Microbiol. Resour. Announc."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"e01980","DOI":"10.1128\/mBio.01980-14","article-title":"Effect of Copper Treatment on the Composition and Function of the Bacterial Community in the Sponge Haliclona cymaeformis","volume":"5","author":"Tian","year":"2014","journal-title":"mBio"},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Lee, L.H., Lui, D., Platner, P.J., Hsu, S.-F., Chu, T.-C., Gaynor, J.J., Vega, Q.C., and Lustigman, B.K. (2006). Induction of Temperate Cyanophage AS-1 by Heavy Metal\u2013Copper. BMC Microbiol., 6.","DOI":"10.1186\/1471-2180-6-17"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"e00125-18","DOI":"10.1128\/CMR.00125-18","article-title":"The Use of Copper as an Antimicrobial Agent in Health Care, Including Obstetrics and Gynecology","volume":"32","author":"Arendsen","year":"2019","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"e99545","DOI":"10.1172\/jci.insight.99545","article-title":"Vaginal Microbiome Modulates Topical Antiretroviral Drug Pharmacokinetics","volume":"3","author":"Taneva","year":"2018","journal-title":"JCI Insight"},{"key":"ref_82","doi-asserted-by":"crossref","unstructured":"Ojala, T., Kankainen, M., Castro, J., Cerca, N., Edelman, S., Westerlund-Wikstr\u00f6m, B., Paulin, L., Holm, L., and Auvinen, P. (2014). Comparative Genomics of Lactobacillus crispatus Suggests Novel Mechanisms for the Competitive Exclusion of Gardnerella vaginalis. BMC Genom., 15.","DOI":"10.1186\/1471-2164-15-1070"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1007\/s43032-023-01351-4","article-title":"Changes in the Vaginal Microbiome During Pregnancy and the Postpartum Period in South African Women: A Longitudinal Study","volume":"31","author":"Li","year":"2023","journal-title":"Reprod. Sci."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"e00410-17","DOI":"10.1128\/IAI.00410-17","article-title":"Microbial Composition Predicts Genital Tract Inflammation and Persistent Bacterial Vaginosis in South African Adolescent Females","volume":"86","author":"Lennard","year":"2018","journal-title":"Infect. Immun."},{"key":"ref_85","doi-asserted-by":"crossref","unstructured":"Mtshali, A., San, J.E., Osman, F., Garrett, N., Balle, C., Giandhari, J., Onywera, H., Mngomezulu, K., Mzobe, G., and De Oliveira, T. (2021). Temporal Changes in Vaginal Microbiota and Genital Tract Cytokines Among South African Women Treated for Bacterial Vaginosis. Front. Immunol., 12.","DOI":"10.3389\/fimmu.2021.730986"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/5\/519\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T04:27:58Z","timestamp":1777696078000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/5\/519"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,30]]},"references-count":85,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2026,5]]}},"alternative-id":["v18050519"],"URL":"https:\/\/doi.org\/10.3390\/v18050519","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,30]]}}}