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.

Transkingdom Analysis of the Female Reproductive Tract Reveals Bacteriophages form Communities

“…We further examined FRT bacteriophage contigs to identify bacteriophage lifestyle and found the majority of identified contigs contained genes consistent with lysogeny. A recent study using metagenomic sequencing to examine the FRT microbiome in South African adolescents also found a high proportion of identified lysogenic phages in the FRT [26]. However, the larger sample size in our study allowed us to further evaluate for the difference by clinical BV diagnosis, revealing significantly more contigs containing lysogenic genes (including integrase, transposase, repressor, and recombinase genes) in BVpositive than BV-negative samples.…”

“…Another group examining a cohort of BV-positive and BVnegative Danish women found no significant difference in viral (including bacteriophage) nor bacterial alpha diversity between BV-positive and BV-negative women [25]. A recent investigation of FRT bacteriophages in South African adolescents showed prevalence and persistence of prophages, but the sample size was small, with only 13 participants [26].…”

Cervicovaginal Human Papillomavirus Genomes, Microbiota Composition and Cytokine Concentrations in South African Adolescents

“…We leveraged previously generated lateral vaginal wall shotgun metagenome sequencing data (i.e., from DNA extracted from swabs without VLP-enrichment, described in Happel et al [ 27 ]) from participants of the same cohort to identify additional complete HPV genomes and report on these here. Briefly, the UW NWGC performed whole metagenome library preparation, quantitation and sequencing of genomic DNA using an Illumina NovaSeq 6000 S4 flow cell.…”

Special Issue: Phage–Bacteria Interplay in Health and Disease

“…Phages also impact human health by infecting bacteria forming human microbiomes in the gut, respiratory tract, skin, or vagina. Happel et al [ 9 ] investigated the prevalence and persistence of (pro)phages and their associations with the vaginal bacterial community composition in the female genital tract of 13 South African adolescents, who received no antibiotics. The shotgun metagenome sequencing of cervicovaginal samples collected longitudinally showed that the most prevalent phage family was Siphoviridae , followed by Myoviridae , Podoviridae , Herelleviridae , and Inoviridae .…”

“…The results pointed out that some prophages were present in cervicovaginal secretions of multiple participants, suggesting that prophages, and thus bacterial strains, are shared between adolescents. Shaping the biodiversity of bacterial populations, these viruses contribute to local fluctuations in the vaginal microbiome [ 9 ].…”