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

Dataset type: Metagenomic
Data released on August 20, 2018

Chen C; Li F; Wei W; Wang Z; Dai J; Hao L; Song L; Zhang X; Zeng L; Du H; Tang H; Liu N; Yang H; Wang J; Madsen L; Brix S; Kristiansen K; Xu X; Li J; Wu R; Jia H (2018): Supporting data for "The metagenome of the female upper reproductive tract" GigaScience Database. http://dx.doi.org/10.5524/100491

DOI10.5524/100491

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.

Additional details

Read the peer-reviewed publication(s):

Chen, C., Li, F., Wei, W., Wang, Z., Dai, J., Hao, L., … Jia, H. (2018). The metagenome of the female upper reproductive tract. GigaScience. doi:10.1093/gigascience/giy107

Accessions (data included in GigaDB):

BioProject: PRJEB24147

Accessions (data not in GigaDB):

BioProject: PRJEB16013
BioProject: PRJEB21098
https: //www.ebi.ac.uk/metabolights/





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
ERS20752051842734  human reproductive system metagenome Description:Shotgun metagenomic sequences from DNA...
Alternative names:C014CVA
Host subject id:C014
...
+
ERS20752061842734  human reproductive system metagenome Description:Shotgun metagenomic sequences from DNA...
Alternative names:C018CVA
Host subject id:C018
...
+
ERS20752091842734  human reproductive system metagenome Description:Shotgun metagenomic sequences from DNA...
Alternative names:C033CVA
Host subject id:C033
...
+
ERS20752101842734  human reproductive system metagenome Description:Shotgun metagenomic sequences from DNA...
Alternative names:C028CVA
Host subject id:C028
...
+
ERS20752111842734  human reproductive system metagenome Description:Shotgun metagenomic sequences from DNA...
Alternative names:C039CVA
Host subject id:C039
...
+
ERS20752121842734  human reproductive system metagenome Description:Shotgun metagenomic sequences from DNA...
Alternative names:C041CVA
Host subject id:C041
...
+
ERS20752131842734  human reproductive system metagenome Description:Shotgun metagenomic sequences from DNA...
Alternative names:C042CVA
Host subject id:C042
...
+
ERS20752141842734  human reproductive system metagenome Description:Shotgun metagenomic sequences from DNA...
Alternative names:C045CVA
Host subject id:C045
...
+
ERS20752151842734  human reproductive system metagenome Description:Shotgun metagenomic sequences from DNA...
Alternative names:C058CVA
Host subject id:C058
...
+
ERS20752161842734  human reproductive system metagenome Description:Shotgun metagenomic sequences from DNA...
Alternative names:C068CVA
Host subject id:C068
...
+
Displaying 1-10 of 76 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
abundanceTEXT1.07 MB2018-08-09
MD5sumUNKNOWN2.89 KB2018-08-09
annotationTEXT1.06 MB2018-08-09
ERS2075272Sequence assemblyFASTA241.62 KB2018-08-09
ERS2075205Sequence assemblyFASTA1.02 MB2018-08-09
ERS2075245Sequence assemblyFASTA257.42 KB2018-08-09
ERS2075206Sequence assemblyFASTA691.89 KB2018-08-09
ERS2075246Sequence assemblyFASTA225.43 KB2018-08-09
ERS2075210Sequence assemblyFASTA3.97 MB2018-08-09
ERS2075247Sequence assemblyFASTA192.28 KB2018-08-09
Displaying 1-10 of 62 File(s).
Date Action
August 20, 2018 Dataset publish
August 20, 2018 Description updated from : 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.
August 21, 2018 Link added : BioProject:PRJEB21098
August 21, 2018 Link added : https://www.ebi.ac.uk/metabolights/
August 28, 2018 Manuscript Link added : 10.1093/gigascience/giy107