Vaginal and fecal microbiome dynamics in menstrual cycle phases

This pilot longitudinal study examined how menstrual cycle phases influence vaginal and fecal bacteriome and mycobiome. Eight reproductively healthy women with regular menstrual cycles self-collected vaginal and stool swabs during the follicular, ovulatory, and luteal phases across three consecutive menstrual cycles. Vaginal fungi were cultured and identified by mass spectrometry, and a total of 72 vaginal and 72 fecal samples were analyzed using qPCR and 16S rRNA. Additionaly, ITS rRNA amplicon sequencing on pooled samples were analyzed. Vaginal bacteriome diversity remained stable across phases, while fecal bacteriome alpha diversity varied, showing the highest values in the luteal phase. Vaginal bacteriome was dominated by Lactobacillus, mainly L. crispatus, with distinct predicted metabolic profiles in communities dominated by L. iners or Gardnerella vaginalis with L. jensenii. Yeasts such as Candida albicans, Nakaseomyces glabratus, and Pichia kudriavzevii were detected. Vaginal yeast presence correlated negatively with L. crispatus and positively with L. iners, and also showed positive associations with fecal Streptococcus. These findings highlight that menstrual cycle phase affects fecal bacteriome composition and reveal notable cross-site associations between vaginal lactobacilli, yeasts, and fecal bacteria, suggesting microbiological links between the vaginal and intestinal environments.