Data from the female urinary microbiota

Dataset type: Metagenomic
Data released on November 19, 2020

Human urine is traditionally considered to be sterile, and whether the urine harbors distinct microbial communities has been a matter of debate. Potential link between female urine and reproductive tract microbial communities is currently not clear.
Here we collected urine samples from 147 Chinese women of reproductive age and explored the nature of colonization by 16S rRNA gene amplicon sequencing, quantitative real-time PCR, and live bacteria culture. To demonstrate the utility of this approach, the intra-individual Spearman's correlation was used to explore the relationship between urine and multiple sites of the female reproductive tract. PERMANOVA was also performed to explore potential correlations between the lifestyle and various clinical factors and urinary bacterial communities. Our data demonstrated distinct bacterial communities in urine, indicative of a non-sterile environment. Streptococcus-dominated, Lactobacillus-dominated and diverse type were the three most common urinary bacterial community types in the cohort. Detailed comparison of the urinary microbiota with multiple sites of the female reproductive tract microbiota demonstrated that the urinary microbiota were more similar to the microbiota in the cervix and uterine cavity than to those of the vagina in the same women.
Our data demonstrate the potential connectivity among microbiota in the female urogenital system and provide insight and resources for exploring diseases of the urethra and genital tract.

Additional details

Read the peer-reviewed publication(s):


Related datasets:

doi:10.5524/100754 IsSupplementTo doi:10.5524/100491

Additional information:

https://doi.org/10.1101/628974

Accessions (data generated as part of this study):

BioProject: PRJEB29341
BioProject: PRJEB36743
CNSA_project: CNP0000166





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
C0011346744  urine metagenome Analyte type:DNA
Alternative accession-CNSA_sample:CNS0012681
CNSA_project:CNP0000166
...
+
C0021346744  urine metagenome Analyte type:DNA
Alternative accession-CNSA_sample:CNS0012666
CNSA_project:CNP0000166
...
+
C0031346744  urine metagenome Analyte type:DNA
Alternative accession-CNSA_sample:CNS0012636
CNSA_project:CNP0000166
...
+
C0041346744  urine metagenome Analyte type:DNA
Alternative accession-CNSA_sample:CNS0012630
CNSA_project:CNP0000166
...
+
C0051346744  urine metagenome Analyte type:DNA
Alternative accession-CNSA_sample:CNS0012603
CNSA_project:CNP0000166
...
+
C0071346744  urine metagenome Analyte type:DNA
Alternative accession-CNSA_sample:CNS0012660
CNSA_project:CNP0000166
...
+
C0081346744  urine metagenome Analyte type:DNA
Alternative accession-CNSA_sample:CNS0012665
CNSA_project:CNP0000166
...
+
C0091346744  urine metagenome Analyte type:DNA
Alternative accession-CNSA_sample:CNS0012637
CNSA_project:CNP0000166
...
+
C0111346744  urine metagenome Analyte type:DNA
Alternative accession-CNSA_sample:CNS0012688
CNSA_project:CNP0000166
...
+
C0121346744  urine metagenome Analyte type:DNA
Alternative accession-CNSA_sample:CNS0012704
CNSA_project:CNP0000166
...
+
Displaying 1-10 of 137 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Tabular DataCSV2.18 MB2020-05-14
Microbial abundancebiom884.38 KB2020-11-12
Tabular dataCSV4.52 KB2020-11-17
Tabular dataCSV7.01 MB2020-11-17
readmeTEXT3.79 KB2020-05-14
Tabular DataCSV16.19 KB2020-05-14
MetadataCSV32.85 KB2020-05-14
ListPDF112.62 KB2020-11-24
Displaying 1-8 of 8 File(s).
Funding body Awardee Award ID Comments
Medical Scientific Research Foundation of Guangdong Weixia Wei A2019035
Shenzhen Municipal Government R Wu SZSM202011016 Sanming Project of Medicine
Shenzhen Municipal Government R Wu SZXK027 Shenzhen Key Medical Discipline Construction Fund

Protocols.io:

Date Action
November 19, 2020 Dataset publish
November 23, 2020 Description updated from : Human urine is traditionally considered to be sterile, and whether the urine harbors distinct microbial communities has been a matter of debate. The potential link between female urine and reproductive tract microbial communities is currently not clear.
Here we collected the urine samples from 147 Chinese women of reproductive age and explored the nature of colonization by 16S rRNA gene amplicon sequencing, quantitative real-time PCR, and live bacteria culture. To demonstrate utility intra-individual Spearman's correlation was used to explore the relationship between urine and multi-sites of the reproductive tract. PERMANOVA was also performed to explore potential correlations between the lifestyle and various clinical factors and urinary bacterial communities. Our data demonstrated distinct bacterial communities in urine, indicative of a non-sterile environment. Streptococcus-dominated, Lactobacillus-dominated and diverse type urinary microbiota were the three most common types in the cohort. Detailed comparison of the urinary microbiota to the multiple sites of female reproductive tract microbiota demonstrated the urinary microbiota was more similar to the microbiota in the cervix and uterine cavity instead of the vagina in the same women.
Our data demonstrate the potential connectivity of the microbiota in the female urogenital system and provided insight into the exploration of urethra and genital tract diseases.
November 24, 2020 Additional file STORMS_Checklist_cc20200910.pdf added
November 24, 2020 File readme_100754.txt updated
February 1, 2021 Manuscript Link added : 10.46471/gigabyte.9