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 Wu; Huijue Jia

doi:10.1093/gigascience/giy107

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

Genomforskning og Molekylær Biomedicin

20 Citationer (Scopus)

48 Downloads (Pure)

Abstract

Background: The human uterus is traditionally believed to be sterile, while the vaginal microbiota plays an important role in fending off pathogens. Emerging evidence demonstrates the presence of bacteria beyond the vagina. However, a microbiome-wide metagenomic analysis characterizing the diverse microbial communities has been lacking.

Results: We performed shotgun-sequencing of 52 samples from the cervical canal and the peritoneal fluid of Chinese women of reproductive age using the Illumina platform. 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 our previous findings in another 24 samples from the vagina, the cervical canal, the uterus and the peritoneal fluid using the BGISEQ-500 platform revealing that microorganisms in the samples from the same individuals were largely shared in the entire reproductive tract. Human sequences made up more than 99% of 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 would require greater depth of sequencing and more samples to meet the full coverage scale.

Conclusions: We provide novel detailed data on the microbial composition of a largely unchartered body site, the female reproductive tract. Our results indicated the presence of an intra-individual continuum of microorganisms that gradually changed from the vagina to the peritoneal fluid. This study also provides a framework for understanding the implications of the composition and functional potential of the distinct microbial ecosystems of the female reproductive tract in relation to health and disease.

Originalsprog	Engelsk
Artikelnummer	giy107
Tidsskrift	GigaScience
Vol/bind	7
Udgave nummer	10
Sider (fra-til)	1-8
ISSN	2047-217X
DOI	https://doi.org/10.1093/gigascience/giy107
Status	Udgivet - 2018

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10.1093/gigascience/giy107Licens: CC BY

The metagenome of the female upper reproductive tractForlagets udgivne version, 799 KBLicens: CC BY

Citationsformater

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title = "The metagenome of the female upper reproductive tract",

abstract = "Background: The human uterus is traditionally believed to be sterile, while the vaginal microbiota plays an important role in fending off pathogens. Emerging evidence demonstrates the presence of bacteria beyond the vagina. However, a microbiome-wide metagenomic analysis characterizing the diverse microbial communities has been lacking.Results: We performed shotgun-sequencing of 52 samples from the cervical canal and the peritoneal fluid of Chinese women of reproductive age using the Illumina platform. 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 our previous findings in another 24 samples from the vagina, the cervical canal, the uterus and the peritoneal fluid using the BGISEQ-500 platform revealing that microorganisms in the samples from the same individuals were largely shared in the entire reproductive tract. Human sequences made up more than 99% of 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 would require greater depth of sequencing and more samples to meet the full coverage scale.Conclusions: We provide novel detailed data on the microbial composition of a largely unchartered body site, the female reproductive tract. Our results indicated the presence of an intra-individual continuum of microorganisms that gradually changed from the vagina to the peritoneal fluid. This study also provides a framework for understanding the implications of the composition and functional potential of the distinct microbial ecosystems of the female reproductive tract in relation to health and disease.",

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

year = "2018",

doi = "10.1093/gigascience/giy107",

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T1 - The metagenome of the female upper reproductive tract

AU - Li, Fei

AU - Chen, Chen

AU - Wei, Weixia

AU - Wang, Zirong

AU - Dai, Juanjuan

AU - Hao, Lilan

AU - Song, Liju

AU - Zhang, Xiaowei

AU - Zeng, Liping

AU - Du, Hui

AU - Tang, Huiru

AU - Liu, Na

AU - Yang, Huanming

AU - Wang, Jian

AU - Madsen, Lise

AU - Brix, Susanne

AU - Kristiansen, Karsten

AU - Xu, Xun

AU - Li, Junhua

AU - Wu, Ruifang

AU - Jia, Huijue

PY - 2018

Y1 - 2018

N2 - Background: The human uterus is traditionally believed to be sterile, while the vaginal microbiota plays an important role in fending off pathogens. Emerging evidence demonstrates the presence of bacteria beyond the vagina. However, a microbiome-wide metagenomic analysis characterizing the diverse microbial communities has been lacking.Results: We performed shotgun-sequencing of 52 samples from the cervical canal and the peritoneal fluid of Chinese women of reproductive age using the Illumina platform. 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 our previous findings in another 24 samples from the vagina, the cervical canal, the uterus and the peritoneal fluid using the BGISEQ-500 platform revealing that microorganisms in the samples from the same individuals were largely shared in the entire reproductive tract. Human sequences made up more than 99% of 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 would require greater depth of sequencing and more samples to meet the full coverage scale.Conclusions: We provide novel detailed data on the microbial composition of a largely unchartered body site, the female reproductive tract. Our results indicated the presence of an intra-individual continuum of microorganisms that gradually changed from the vagina to the peritoneal fluid. This study also provides a framework for understanding the implications of the composition and functional potential of the distinct microbial ecosystems of the female reproductive tract in relation to health and disease.

AB - Background: The human uterus is traditionally believed to be sterile, while the vaginal microbiota plays an important role in fending off pathogens. Emerging evidence demonstrates the presence of bacteria beyond the vagina. However, a microbiome-wide metagenomic analysis characterizing the diverse microbial communities has been lacking.Results: We performed shotgun-sequencing of 52 samples from the cervical canal and the peritoneal fluid of Chinese women of reproductive age using the Illumina platform. 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 our previous findings in another 24 samples from the vagina, the cervical canal, the uterus and the peritoneal fluid using the BGISEQ-500 platform revealing that microorganisms in the samples from the same individuals were largely shared in the entire reproductive tract. Human sequences made up more than 99% of 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 would require greater depth of sequencing and more samples to meet the full coverage scale.Conclusions: We provide novel detailed data on the microbial composition of a largely unchartered body site, the female reproductive tract. Our results indicated the presence of an intra-individual continuum of microorganisms that gradually changed from the vagina to the peritoneal fluid. This study also provides a framework for understanding the implications of the composition and functional potential of the distinct microbial ecosystems of the female reproductive tract in relation to health and disease.

U2 - 10.1093/gigascience/giy107

DO - 10.1093/gigascience/giy107

M3 - Journal article

C2 - 30192933

AN - SCOPUS:85054761818

SN - 2047-217X

VL - 7

SP - 1

EP - 8

JO - GigaScience

JF - GigaScience

IS - 10

M1 - giy107

ER -

The metagenome of the female upper reproductive tract

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