The metagenome of the female upper reproductive tract

Fei Li, Chen Chen, Weixia Wei, Zirong Wang, Juanjuan Dai, Lilan Hao, Liju Song, Xiaowei Zhang, Liping Zeng, Hui Du, Huiru Tang, Na Liu, Huanming Yang, Jian Wang, Lise Madsen, Susanne Brix, Karsten Kristiansen, Xun Xu, Junhua Li, Ruifang WuHuijue Jia*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Background: 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.
Results: We performed shotgun-sequencing using the Illumina platform of 52 samples from the cervical canal and 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 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.
Conclusions: Microbiota in unprecedented data for unchartered body site, female upper reproductive tract, were analyzed in this study. The community results indicated that an intra-individual continuum of all types of microorganisms gradually changed from the vagina to the peritoneal fluid. A framework was also established in this study aiming at understanding the implications of the composition and functional potential of this distinct microbial ecosystem in relation to health and disease.
Original languageEnglish
Article numbergiy107
Issue number10
Number of pages8
Publication statusPublished - 2018

Bibliographical note

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (


  • Metagenomics
  • Microbiota
  • Female upper reproductive tract


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