Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Urine Urine,urine
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Hormone replacement therapy HORMONE REPLACE THER,Hormone Replacement Therapies,Hormone Replacement Therapy,REPLACE THER HORMONE,Replacement Therapies, Hormone,Replacement Therapy, Hormone,THER HORMONE REPLACE,Therapies, Hormone Replacement,Therapy, Hormone Replacement,Hormone replacement therapy,hormone replacement therapy
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- EHT- Group (Premenopausal women in the 'No UTI History and rUTI History( UTI(−) cohorts' who did not use estrogen hormone therapy (EHT))
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- EHT+ Group (Premenopausal women in the 'No UTI History and rUTI History( UTI(−) cohorts' who used estrogen hormone therapy (EHT))
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Premenopausal women in the 'No UTI History and rUTI History( UTI(−) cohorts' with systemic and vaginal estrogen hormone therapy (EHT) who did not have UTI at the time of urine donation.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Sanger
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4.5
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22
Source: Fig 4C + 4H
Description: Urogenital microbiomes of EHT(+) (aggregated systemic and vaginal) women compared to those of EHT(−) women
Abundance in Group 1: increased abundance in EHT+ Group (Premenopausal women in the 'No UTI History and rUTI History( UTI(−) cohorts' who used estrogen hormone therapy (EHT))
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Lactobacillus crispatus | ||
| Limosilactobacillus vaginalis |
Revision editor(s): Tolulopeo, Chinelsy, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22
Curated date: 2023/10/25
Curator: Tolulopeo
Revision editor(s): Tolulopeo, OdigiriGreat, ChiomaBlessing
Source: Fig 4H
Description: Urogenital microbiomes of EHT(+) women compared to those of EHT(-) women
Abundance in Group 1: increased abundance in EHT+ Group (Premenopausal women in the 'No UTI History and rUTI History( UTI(−) cohorts' who used estrogen hormone therapy (EHT))
| NCBI | Quality Control | Links |
|---|---|---|
| Fannyhessea vaginae | ||
| Streptococcus infantis | ||
| Streptococcus mitis | ||
| Streptococcus oralis | ||
| Streptococcus pneumoniae |
Revision editor(s): Tolulopeo, OdigiriGreat, ChiomaBlessing
