Metagenome of the female upper reproductive tract

Background The human uterus is traditionally believed to be sterile, while the vaginal microbiota plays important roles in fending off pathogens. Emerging evidences demonstrate the presence of bacteria beyond the vagina, but currently there is no support from metagenomic data. Results Here we shotgun-sequence over 50 samples from the cervical canal and the peritoneal fluid of Chinese women of reproductive age, who were operated for conditions not known to involve infection. With 20GB sequences per sample and an average rate of >99% human sequences, vaginal bacteria could be well covered, while a full characterization of bacteria from the upper reproductive tract would require a greater amount of sequences and more samples. Direct annotation of sequencing reads identified bacteria, archaea, fungi and viruses from the samples, confirming as well as extending results from 16S rRNA gene amplicon sequencing. To further examine transitions between communities at neighboring sites, another 24 samples from the vagina, the cervical canal, the uterus and the peritoneal fluid were shotgun-sequenced. Samples from the same individual share a large portion of this microbiota. Conclusions Our metagenomic analysis of the microbiota of the female upper reproductive tract provides unprecedented data for this unchartered body site and establishes the framework for future studies aimed at understanding the composition and functional capacity of this community or its specific members.