The vagino-cervical microbiome as a woman\'s life history

The gut microbiome has been the center of attention for human commensal microbiome studies. For the vagina, another densely populated body site, 16S rRNA gene amplicon sequencing studies have identified community types and observed dynamic changes related to menstrual cycles and sexual behaviors in small cohorts. Here we perform metagenomic shotgun sequencing on cervical samples from 1148 volunteers (a cohort more than 20-fold of the Human Microbiome Project (HMP)). Factors such as pregnancy and delivery histories and contraception methods were all more important than menstrual cycle, and contributing to non-Lactobacilli bacterial or viral species in the vagino-cervical microbiome. Bifidobacterium was seen with older age at sexual debut or marriage; Streptococcus agalactiae was found in those who suffered a heavy menstrual flow. Other features such as mood fluctuations and facial speckles could potentially be deduced from the vagino-cervical microbiome. Lactobacillus crispatus and Prevotella bivia could be shared between the gut and the vagino-cervical microbiome. Oral microbiome, plasma vitamins, metals, amino acids and hormones showed clear associations with the vagino-cervical microbiome. Our results offer an unprecedented glimpse into the microbiota of the female reproductive tract and point to disease susceptibilities that may be relieved by behavioral changes.