Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents

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dc.contributor.authorHappel, Anna-Ursula
dc.contributor.authorBalle, Christina
dc.contributor.authorMaust, Brandon S
dc.contributor.authorKonstantinus, Iyaloo N
dc.contributor.authorGill, Katherine
dc.contributor.authorBekker, Linda-Gail
dc.contributor.authorFroissart, Rémy
dc.contributor.authorPassmore, Jo-Ann
dc.contributor.authorKaraoz, Ulas
dc.contributor.authorVarsani, Arvind
dc.contributor.authorJaspan, Heather
dc.date.accessioned2022-04-04T08:26:35Z
dc.date.available2022-04-04T08:26:35Z
dc.date.issued2021-11-23
dc.date.updated2021-12-23T15:06:36Z
dc.description.abstractThe 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. <i>Siphoviridae</i> was the most prevalent bacteriophage family, followed by <i>Myoviridae</i>, <i>Podoviridae</i>, <i>Herelleviridae</i>, and <i>Inoviridae</i>. 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 <i>Gardnerella</i> than <i>Lactobacillus</i> 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.en_US
dc.identifierdoi: 10.3390/v13122341
dc.identifier.apacitationHappel, A., Balle, C., Maust, B. S., Konstantinus, I. N., Gill, K., Bekker, L., ... Jaspan, H. (2021). Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents. <i>Viruses</i>, 13(12), 2341. http://hdl.handle.net/11427/36254en_ZA
dc.identifier.chicagocitationHappel, Anna-Ursula, Christina Balle, Brandon S Maust, Iyaloo N Konstantinus, Katherine Gill, Linda-Gail Bekker, Rémy Froissart, et al "Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents." <i>Viruses</i> 13, 12. (2021): 2341. http://hdl.handle.net/11427/36254en_ZA
dc.identifier.citationHappel, A., Balle, C., Maust, B.S., Konstantinus, I.N., Gill, K., Bekker, L., Froissart, R. & Passmore, J. et al. 2021. Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents. <i>Viruses.</i> 13(12):2341. http://hdl.handle.net/11427/36254en_ZA
dc.identifier.ris TY - Journal Article AU - Happel, Anna-Ursula AU - Balle, Christina AU - Maust, Brandon S AU - Konstantinus, Iyaloo N AU - Gill, Katherine AU - Bekker, Linda-Gail AU - Froissart, Rémy AU - Passmore, Jo-Ann AU - Karaoz, Ulas AU - Varsani, Arvind AU - Jaspan, Heather AB - 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. <i>Siphoviridae</i> was the most prevalent bacteriophage family, followed by <i>Myoviridae</i>, <i>Podoviridae</i>, <i>Herelleviridae</i>, and <i>Inoviridae</i>. 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 <i>Gardnerella</i> than <i>Lactobacillus</i> 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. DA - 2021-11-23 DB - OpenUCT DP - University of Cape Town IS - 12 J1 - Viruses KW - : bacteriophages KW - prophages KW - lytic KW - vaginal microbiota KW - stability KW - CRISPR KW - Sub-Saharan Africa LK - https://open.uct.ac.za PY - 2021 T1 - Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents TI - Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents UR - http://hdl.handle.net/11427/36254 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/36254
dc.identifier.vancouvercitationHappel A, Balle C, Maust BS, Konstantinus IN, Gill K, Bekker L, et al. Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents. Viruses. 2021;13(12):2341. http://hdl.handle.net/11427/36254.en_ZA
dc.language.isoenen_US
dc.publisher.departmentDivision of Infectious Disease and HIV Meden_US
dc.publisher.facultyFaculty of Health Sciencesen_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.sourceVirusesen_US
dc.source.journalissue12en_US
dc.source.journalvolume13en_US
dc.source.pagination2341en_US
dc.source.urihttps://www.mdpi.com/journal/viruses
dc.subject: bacteriophagesen_US
dc.subjectprophages
dc.subjectlytic
dc.subjectvaginal microbiota
dc.subjectstability
dc.subjectCRISPR
dc.subjectSub-Saharan Africa
dc.titlePresence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescentsen_US
dc.typeJournal Articleen_US
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