The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection.

In this study we examined potential associations of HPV infection with the cervical microbiota. Cervical samples were collected from 87 HIV-seronegative reproductive-age Black South African women. Microbiota were characterized by Illumina sequencing of the V3-V4 hypervariable regions of the bacterial 16S rRNA gene. Thirty seven (42.5%) and 30 (34.5%) of the women had prevalent HPV and high-risk (HR)-HPV, respectively. Only 23 women (26.4%) had cervical microbiota dominated by a single Lactobacillus species (L. crispatus (2/87 (2.3%)), L. jensenii (2/87 (2.3%)), and L. iners (19/87 (21.8%)). The majority of the women (56/87 (64.4%)) had diverse cervical microbiota consisting of mainly bacterial vaginosis-associated bacteria. The remaining women (8/87 (9.2%)) had microbiota dominated by Aerococcus, Streptococcus, Chlamydia or Corynebacterium. Women with HR-HPV had significantly higher relative abundances of Aerococcaceae, Pseudomonadaceae and Bifidobacteriaceae compared to those with low-risk (LR)-HPV or no HPV-infection (LDA score >2.0, p < 0.05, q < 0.2). Gardnerella, Sneathia, and Atopobium were also found at greater relative abundances in HR-HPV-infected women compared to those with low-risk (LR)-HPV or no HPV-infection (LDA score >2.0, p < 0.05), although the difference was not significant after FDR-adjustment (q > 0.2). Further investigations of the bacterial taxa significantly enriched in HR-HPV-infected women are warranted.