Reproductive microbiome in women with PCOS and the menstrual cycle

Similar to the gut microbiome, alterations in the reproductive tract (RT) microbial community are associated not only with gynecological diseases, such as bacterial vaginosis (BV), chronic endometritis, and endometriosis, but also with reproductive complications, such as in vitro fertilization failure.However, the majority of research on the RT microbiome has focused on the vaginal microbiome, leaving a significant gap in our understanding of the endometrial microbiome. For example, studies have reported alterations in vaginal microbiome in women with PCOS. In contrast, the endometrial microbiome in PCOS still remains unexplored. Research on the RT microbiome, which could have a more direct impact than the gut microbiome, has received less attention compared to studies on the gut microbiome.In this study, we aim to characterize the lower and upper RT microbiome using endometrial fluid (EF) and vaginal swab (VS) samples and to analyze the associations between the obtained microbial compositions and PCOS/the menstrual cycle. Furthermore, we also investigate the agreement in the microbiome profiles for detecting signals specific to PCOS and the Cycle phases. This is the first study to explore the upper RT microbiome in women with PCOS across menstrual cycles.A total of 545 genera were detected in the EF microbiome, while 114 genera were in the VS microbiome. Lactobacillus was the dominant taxa in both EF and VS samples. Our first aim was to compare the profiles of the upper and lower RT microbiome obtained through the two sampling methods. The EF microbial community exhibited significantly higher alpha diversity and distinct clustering from the VS community. Furthermore, we uncovered individual-specific variability through Aitchison distance analysis.Next, we analyzed the associations between the RT microbiome, PCOS, and the menstrual cycle phases. We observed no statistically significant differences in alpha diversity regarding the PCOS status in either EF or VS profiles. On the other hand, the cycle phases were significantly associated with the microbiome alpha diversity, showing a discernible decreasing trend from the proliferative to secretory phases. Again, there were no difference in beta diversity concerning PCOS or the cycle.To study microbiome alterations related to PCOS and the cycle phases, we focused on all pairwise-log ratios between two bacterial genera. we identified 2 log-ratios associated with PCOS and 13 log-ratios with the menstrual cycle phases only in the EF samples. Last, we calculated the effect sizes to assess the effects of PCOS and the cycle on these log-ratios. While the effect sizes for PCOS from both EF and VS were uncorrelated, the effect sizes for the cycle phases showed a strong correlation, indicating that the profile of the upper and lower RT microbiome is associated with the cycle phases.