Changes in the vaginal microbiome during pregnancy and the postpartum period in South African women: a longitudinal study

African women have more diverse vaginal microbiota than women of European descent, and there is interest in the impact of this diversity on maternal health, including HIV and STI acquisition. We characterized the vaginal microbiota in a cohort of women ≥ 18 years with and without HIV in a longitudinal cohort over two visits during pregnancy and one visit postpartum. At each visit we obtained HIV testing and self-collected vaginal swabs for point of care testing for STIs and microbiome sequencing. We categorized microbial communities and evaluated changes over pregnancy and associations with HIV status and STI diagnosis. Across 242 women (mean age 29,44% living with HIV, 33% diagnosed with STIs), we identified four main community state types (CSTs): two lactobacillus-dominant CSTs (dominated by Lactobacillus crispatus and Lactobacillus iners respectively) and two diverse, non-lactobacillus-dominant CSTs (one dominated by Gardnerella vaginalis and one by other facultative anaerobes). From first antenatal visit to third trimester (24–36 weeks gestation), 60% of women in the Gardnerella-dominant CST shifted to Lactobacillus-dominan CSTs. From third trimester to postpartum (mean 17 days post-delivery), 80% of women in Lactobacillus-dominant CSTs shifted to non-lactobacillus-dominant CSTs with a large proportion in the facultative anaerobe-dominant CST. Microbial composition differed by STI diagnosis (PERMANOVA R(2) = 0.002, p = 0.004), and women diagnosed with an STI were more likely to be categorized with L. iners-dominant or Gardnerella-dominant CSTs. Overall we found a shift toward lactobacillus dominance during pregnancy, and the emergence of a distinct, highly diverse anaerobe-dominant microbiome population in the postpartum period.