Methods
During 2-years of follow-up, 108 women provided 2,662 vaginal samples. Participants reported three HC methods [oral contraceptive pill (OCP), vaginal ring, implanon]. Controls not taking HC were also followed. Visits were scheduled at baseline, 2 and 4 weeks, 3, 6, 12, 18, and 24 months. Participants self-collected mid-vaginal swabs twice-weekly in the two weeks prior to each visit. Vaginal microbiota composition was characterized on all samples by 16S rRNA gene sequencing of the V3-V4 hypervariable regions. We identified four community state types (CSTs) which were dominated by Lactobacillus spp. (CST I, II, III, V). CST-IV-B was characterized by a low relative abundance of Lactobacillus spp. and higher proportions of BV-associated bacteria (Gardnerella and Atopobium), whereas CST-IV-A was dominated by various anaerobic bacteria including Anaerococcus, Peptoniphilus and Prevotella. A multinomial model was used to evaluate the association between proportions of CST and HC. Jensen-Shannon distances between all pairs of samples were analyzed to assess stability of the microbiota longitudinally.
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