Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- urinary tract infection INFECTION, URINARY TRACT,TRACT, INFECTION OF URINARY,urinary tract infection,urinary tract infection (disease)
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No UTI History
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- rUTI History, UTI (-), rUTI History, UTI(+)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Consists of post menopausal (PM) women with a recent history of recurring urinary tract infection ( rUTI) but no active UTI at the time of urine donation (rUTI History, UTI(−)), and(rUTI History, UTI(+))consisted of PM women with a history of rUTI and an active, symptomatic UTI at the time of urine donation respectively
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 50
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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, Matched on: "Urine pH" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Urine pH, Matched on: "Urinary Creatinine concentration" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Urinary Creatinine concentration, Matched on: "smoking history" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.smoking history
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "sample size" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.sample size, Confounders controlled for: "Uncomplicated UTI" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Uncomplicated UTI, Confounders controlled for: "UTI History" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.UTI History
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Fig 3B
Description: Differentially abundant taxa between the No UTI History and rUTI History, UTI(−) groups using BMDA .
Abundance in Group 1: increased abundance in rUTI History, UTI (-), rUTI History, UTI(+)
| NCBI | Quality Control | Links |
|---|---|---|
| Aerococcus | ||
| Lactobacillus |
Revision editor(s): Tolulopeo
Signature 2
Source: Fig 3E
Description: Comparison of differentially abundant taxa between the rUTI History, UTI(−) group the No UTI History
Abundance in Group 1: increased abundance in rUTI History, UTI (-), rUTI History, UTI(+)
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Premenopausal women with no UTI History and rUTI History( UTI(−) groups) without estrogen hormone therapy (EHT)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- EHT+ Premenopausal women with no UTI History and rUTI History( UTI(−) groups) with estrogen hormone therapy (EHT)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Premenopausal women with no UTI History and rUTI History( UTI(−) groups) 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
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.0032
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
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
- increased
Signature 1
Source: Fig 4H
Description: Urogenital microbiomes of EHT(+) (aggregated systemic and vaginal) women compared to those of EHT(−) women using BMDA model
Abundance in Group 1: increased abundance in EHT+ Premenopausal women with no UTI History and rUTI History( UTI(−) groups) with estrogen hormone therapy (EHT)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Lactobacillus crispatus | ||
| Limosilactobacillus vaginalis |
Signature 2
Source: Fig 4H
Description: Urogenital microbiomes of EHT(−) women compared to those of EHT(+) (aggregated systemic and vaginal) women using the BMDA model.
Abundance in Group 1: increased abundance in EHT+ Premenopausal women with no UTI History and rUTI History( UTI(−) groups) with estrogen hormone therapy (EHT)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus infantis | ||
| Streptococcus mitis | ||
| Streptococcus oralis | ||
| Streptococcus pneumoniae | ||
| Fannyhessea vaginae |
Revision editor(s): Tolulopeo, OdigiriGreat
Signature 3
Source: Fig 4G
Description: Urogenital microbiomes of EHT(+) (aggregated systemic and vaginal) women compared to those of EHT(−) women using LEfSe model
Abundance in Group 1: increased abundance in EHT+ Premenopausal women with no UTI History and rUTI History( UTI(−) groups) with estrogen hormone therapy (EHT)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
Revision editor(s): Tolulopeo
Signature 4
Source: Fig 4H
Description: Urogenital microbiomes of EHT(−) women compared to those of EHT(+) (aggregated systemic and vaginal) women using LEfSe model
Abundance in Group 1: increased abundance in EHT+ Premenopausal women with no UTI History and rUTI History( UTI(−) groups) with estrogen hormone therapy (EHT)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus |
Revision editor(s): Tolulopeo
Signature 5
Source: Fig 4A
Description: Relative abundance of the top 22 bacterial genera among EHT(−) (n = 21) and EHT(+) (n = 29) women in the No UTI History and rUTI History, UTI(−) groups.
Abundance in Group 1:Revision editor(s): Tolulopeo
Signature 6
Source: Fig 4B
Description: Species-level taxonomic profiles of the relative abundance of the top 22 bacterial genera among EHT(−) (n = 21) and EHT(+) (n = 29) women in the No UTI History and rUTI History, UTI(−) groups.
Abundance in Group 1:
