Supporting data for "The metagenome of the female upper reproductive tract"

The human uterus is traditionally believed to be sterile, while the vaginal microbiota plays important role in fending off pathogens. Emerging evidence demonstrates the presence of bacteria beyond the vagina. However, a microbiome-wide metagenomic analysis identifying the overall microorganism communities has been lacking. We performed shotgun-sequencing by Illumina platform of 52 samples from the cervical canal and the peritoneal fluid of Chinese women in reproductive age. Direct annotation of sequencing reads identified the taxonomy of bacteria, archaea, fungi and viruses, confirming and extending the results from our previous study. We replicated the findings in another 24 samples from the vagina, the cervical canal, the uterus and the peritoneal fluid using BGISEQ-500 platform, revealing that microorganisms in the samples from the same individual were largely shared in the whole reproductive tract. Over 99% human sequences were detected in the 20GB raw data. After filtering, vaginal microorganisms were well covered in the generated reproductive tract gene catalogue, while the more diverse upper reproductive tract microbiota might need greater depth of sequencing and more samples to meet the full coverage scale.