Metagenome of the female upper reproductive tract

BackgroundThe human uterus is traditionally believed to be sterile, while the vaginal microbiotaplays important roles in fending off pathogens. Emerging evidences demonstrate thepresence of bacteria beyond the vagina, but currently there is no support frommetagenomic data.ResultsHere we shotgun-sequence over 50 samples from the cervical canal and the peritonealfluid of Chinese women of reproductive age, who were operated for conditions notknown to involve infection. With 20GB sequences per sample and an average rate of>99% human sequences, vaginal bacteria could be well covered, while a fullcharacterization of bacteria from the upper reproductive tract would require a greateramount of sequences and more samples. Direct annotation of sequencing readsidentified bacteria, archaea, fungi and viruses from the samples, confirming as well asextending results from 16S rRNA gene amplicon sequencing. To further examinetransitions between communities at neighboring sites, another 24 samples from thevagina, the cervical canal, the uterus and the peritoneal fluid were shotgun-sequenced.Samples from the same individual share a large portion of this microbiota.ConclusionsOur metagenomic analysis of the microbiota of the female upper reproductive tractprovides unprecedented data for this unchartered body site and establishes theframework for future studies aimed at understanding the composition and functionalcapacity of this community or its specific members.