Background The vaginal microbiota can be clustered into six community state types (CSTs): 4 are dominated by Lactobacillus iners, L. crispatus, L. gasseri, L. jensenni, and 2 lack significant numbers of Lactobacillusspp. (termed CST IV-A and IV-B). CST IV-A is characterised by a diverse assemblage of strict anaerobes, while CST IV-B has higher proportions of the genera Atopobium, Gardnerella,among others. We sought to describe the relationship between vaginal microbiota and human papillomavirus (HPV) detection.

Methods Thirty-two reproductive-age women self-collected mid-vaginal swabs twice-weekly for 16 weeks (n = 937 samples). Participants reported behaviours on daily diaries. Vaginal bacterial communities were characterised by pyrosequencing of barcoded 16S rRNA genes (V1-V2 region). Each swab was tested for 37 types of HPV DNA using the Roche HPV Linear Array genotyping test. The effects of CSTs on the rate of transition between HPV-negative and HPV-positive states were assessed using continuous-time Markov models. Additive mixed effects logistic regression and additive mixed effects Poisson models were used to model high risk HPV (hrHPV) and count of HPV types, respectively, with normalised menstrual cycle time.

Results Participants had an average of 29 (range 25–33) samples tested for HPV, with point prevalence ranging from 58 to 77% and 16-week period prevalence of 84%. CST was significantly associated with changes in HPV status (p < 0.001). L. gasseri-dominated CSTs had the fastest HPV remission rate (HPV-positive to no detection) and CST IV-B had the slowest rate compared to L. crispatus-dominated CSTs (adjusted transition rate ratio (aTRR):7.58, 95% CI: 1.77–32.42 and aTRR:0.31, 95% CI: 0.09–1.05, respectively). Detection of hrHPV and count of different HPV types were highest in the middle of the menstrual cycle.

Conclusion Vaginal microbiota dominated by L. gasseriwere associated with increased clearance of detectable HPV. A mid-cycle increase in HPV detection suggests a role for sex hormones in modulating latent infection.