Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents
Abstract
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.
- Authors:
-
[1];
[1];
[2];
[5];
[8];
[9]
- Univ. of Cape Town (South Africa)
- Seattle Children’s Research Institute, Seattle, WA (United States); University of Washington School of Medicine, Seattle, WA (United States)
- Univ. of Cape Town (South Africa); Namibia Institute of Pathology (Namibia)
- Univ. of Cape Town (South Africa); Centre for the AIDS Programme of Research in South Africa (CAPRISA) (South Africa)
- Montpellier Univ. (France)
- Univ. of Cape Town (South Africa); Centre for the AIDS Programme of Research in South Africa (CAPRISA) (South Africa); National Health Laboratory Service (South Africa)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth and Environmental Science
- Arizona State Univ., Tempe, AZ (United States); Univ. of Cape Town (South Africa)
- Univ. of Cape Town (South Africa); Seattle Children’s Research Institute, Seattle, WA (United States); University of Washington School of Medicine, Seattle, WA (United States); University of Washington School of Public Health Seattle, WA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Climate and Environmental Sciences Division; South African Medical Research Council (MRC); National Institutes of Health (NIH); European Union (EU); National Science Foundation (NSF)
- OSTI Identifier:
- 1895334
- Grant/Contract Number:
- AC02-05CH11231; DBI-0735191; DBI-1265383; DBI-1743442
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Viruses
- Additional Journal Information:
- Journal Volume: 13; Journal Issue: 12; Journal ID: ISSN 1999-4915
- Publisher:
- MDPI
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; bacteriophages; prophages; lytic; vaginal microbiota; stability; CRISPR; Sub-Saharan Africa
Citation Formats
Happel, Anna-Ursula, Balle, Christina, Maust, Brandon S., Konstantinus, Iyaloo N., Gill, Katherine, Bekker, Linda-Gail, Froissart, Rémy, Passmore, Jo-Ann, Karaoz, Ulas, Varsani, Arvind, and Jaspan, Heather. Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents. United States: N. p., 2021.
Web. doi:10.3390/v13122341.
Happel, Anna-Ursula, Balle, Christina, Maust, Brandon S., Konstantinus, Iyaloo N., Gill, Katherine, Bekker, Linda-Gail, Froissart, Rémy, Passmore, Jo-Ann, Karaoz, Ulas, Varsani, Arvind, & Jaspan, Heather. Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents. United States. https://doi.org/10.3390/v13122341
Happel, Anna-Ursula, Balle, Christina, Maust, Brandon S., Konstantinus, Iyaloo N., Gill, Katherine, Bekker, Linda-Gail, Froissart, Rémy, Passmore, Jo-Ann, Karaoz, Ulas, Varsani, Arvind, and Jaspan, Heather. Tue .
"Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents". United States. https://doi.org/10.3390/v13122341. https://www.osti.gov/servlets/purl/1895334.
@article{osti_1895334,
title = {Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents},
author = {Happel, Anna-Ursula and Balle, Christina and Maust, Brandon S. and Konstantinus, Iyaloo N. and Gill, Katherine and Bekker, Linda-Gail and Froissart, Rémy and Passmore, Jo-Ann and Karaoz, Ulas and Varsani, Arvind and Jaspan, Heather},
abstractNote = {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.},
doi = {10.3390/v13122341},
journal = {Viruses},
number = 12,
volume = 13,
place = {United States},
year = {Tue Nov 23 00:00:00 EST 2021},
month = {Tue Nov 23 00:00:00 EST 2021}
}
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