Longitudinal profiling and correlations of vaginal and fecal microbiomes throughout the menstrual cycle: A pilot prospective study

Hormonal and endometrial fluctuations across the menstrual cycle may influence both vaginal and fecal microbiomes. Since no longitudinal study examining both matrices together in this context exists, our study aimed to evaluate microbiome changes in three phases of the menstrual cycle and to investigate correlations between bacteriomes and mycobiomes in vaginal and fecal samples. Over the course of three consecutive menstrual cycles, vaginal and stool swabs were self-collected in the follicular, ovulatory, and luteal phases from eight parous women of reproductive age who had regular menstrual cycle. Microscopic fungi in all vaginal samples were cultured and identified by mass spectrometry. DNA from 72 vaginal and 72 fecal samples were analyzed using quantitative PCRs, 16S and ITS rRNA amplicon sequencing for bacteriome and mycobiome profiling. Metabolic pathways were analyzed with a focus on the members of the Lactobacillaceae family. Bacteriome diversity in vaginal samples remained stable across studied months and individual phases, while changes in bacteriome alpha diversity (Shannon index) across phases were observed in fecal samples, with the highest diversity observed during the luteal phase. As expected, the genus Lactobacillus (mostly L. crispatus ) predominated in the vaginal samples. Furthermore, different patterns of the predicted metabolic potential were observed in vaginal samples dominated by Lactobacillus iners or Gardnerella vaginalis with Lactobacillus jensenii , compared to the profile dominated by L. crispatus . Yeasts, such as Candida albicans , Nakaseomyces glabratus , and Pichia kudriavzevii , were found in some vaginal samples. The presence of vaginal yeasts correlated with relative abundances of L. crispatus (negatively) and L. iners (positively) in vaginal samples, and with genus Streprococcus in stool samples (positively). Relative abundances of L. jensenii in vaginal samples correlated with genera Bifidobacterium (negatively) and Dialister (positively) in stool samples. The results indicate that when investigating female fecal microbiome, the phase of menstrual cycle should be considered. Some strong correlations between the relative abundance/presence of vaginal lactobacilli and yeasts and fecal bacteria were found, suggesting a possible link between the composition of microbial communities of these two anatomical sites.