We systematically sample the microbiota in the female reproductive tract from a large cohort of Chinese women of reproductive age using 16S rRNA gene sequencing, conventional bacterial culture and real-time PCR, and demonstrate a continuity of the vagino-uterine microbiome.

Human fetuses are long believed to grow in a sterile environment until birth, when they receive their mothers’ vaginal microbiota. Bacteria have been detected in umbilical cord, amniotic fluid and placenta, which is as yet not viewed as a normal condition. Here we systematically sample the microbiota throughout the female reproductive tract, and uncover diverse microbes from the cervix, uterus, fallopian tubes and peritoneal fluid, which are distinct from the vaginal microbiota but mirror their anatomical contingency with each other. Microbial taxa and potential functions correlated with menstrual cycle, or over-represented in subjects with adenomyosis, and infertility due to endometriosis are identified. Correlations between urine metabolites and microbiota components were also found. The study presents a framework for future endeavors in understanding the relationship between the vagino-uterine microbiome and the health of women and infants, and in the development of novel tests for the microbiome-related conditions.