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

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

doi:10.3390/v13122341

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

Journal Article · Mon Nov 22 23:00:00 EST 2021 · Viruses

DOI:https://doi.org/10.3390/v13122341· OSTI ID:1895334

^[1]; ^[1]; ^[2]; Konstantinus, Iyaloo N. ^[3]; Gill, Katherine ^[4]; Bekker, Linda-Gail ^[4]; ^[5]; Passmore, Jo-Ann ^[6]; Karaoz, Ulas ^[7]; ^[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)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: 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)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1895334

Journal Information:: Viruses, Journal Name: Viruses Journal Issue: 12 Vol. 13; ISSN 1999-4915

Publisher:: MDPICopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
CRISPR
Sub-Saharan Africa
bacteriophages
lytic
prophages
stability
vaginal microbiota

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

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