A case-control study of the vaginal, cervical, and endometrial microbiome in women who have a history of infertility using 16S rRNA amplicon sequencing

Background: The human vaginal microbiome is critical for local homeostasis and defence against pathogens. However, far less is known about the microbiome inhabiting the upper female reproductive tract and its impact on fertility. Here we have examined the association of the vaginal, cervical, and endometrial microbiota for women with a history of infertility compared to women with a history of fertility using a case-control study design. Results: A total of 68 specimens from the reproductive tracts of 33 women were analysed using 16s RNA amplicon sequencing (18 controls and 15 cases). The dominant microbial community members were consistent in the vagina and cervix specimens for all 24 women of the 33 women where sequences were obtained from both sites. However, for the 11 women where endometrial sequences were obtained, there were significantly different proportions of these most abundant taxa relative to that in the individuals vaginal specimens (p=0.0264). When the microbial communities were analysed using the previously described reproductive tract community state types, three endometrial specimens formed a separate cluster within community state type IV. In addition, Ureaplasma spp. was found to be over-represented in the vaginal and cervical microbiota of women with a history of infertility (p=0.011-0.42 (unadjusted)). This was further confirmed using a separate PCR that also validated that the species was Ureaplasma parvum, additionally women with Ureaplasma were more likely to have Lactobacillus iners. When we examined expression of selected genes in the endometrium there was no evidence of case-control status, or microbial community composition, correlating with their expression, but Tenascin-C expression significantly correlated with a history of miscarriage. Conclusions: The presence and structure of the microbial communities in the upper female reproductive tract is not always the same as the lower reproductive tract, and it may have important implications for fertility and outcomes of assisted reproductive technologies.