Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome

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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22

Curated date: 2023/10/09

Curator: Tolulopeo

Revision editor(s): Tolulopeo, ChiomaBlessing

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: Urinary tract infection INFECTION, URINARY TRACT,TRACT, INFECTION OF URINARY,urinary tract infection,urinary tract infection (disease),Urinary tract infection

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 (-)

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(−))

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: 25

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: Negative Binomial Regression

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

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

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22

Curated date: 2023/10/25

Curator: Tolulopeo

Revision editor(s): Tolulopeo, ChiomaBlessing

Source: Fig 3D + 3E

Description: Differentially abundant taxa in the rUTI History, UTI(−) group compared to the No UTI History group

Abundance in Group 1: increased abundance in rUTI History, UTI (-)

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Aerococcus
Anaerococcus lactolyticus
Anaerococcus vaginalis
Lactobacillus
Lactobacillus crispatus
Limosilactobacillus vaginalis
Aerococcus urinae

Revision editor(s): Tolulopeo, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22

Curated date: 2023/10/25

Curator: Tolulopeo

Revision editor(s): Chloe, ChiomaBlessing, Tolulopeo, Chinelsy

Source: Fig 3D + 3E

Description: Differentially abundant taxa in the rUTI History, UTI(−) group compared to the No UTI History group

Abundance in Group 1: increased abundance in rUTI History, UTI (-)

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Anaerococcus hydrogenalis
Anaerococcus prevotii
Bacteroides
Bacteroides uniformis
Brevibacterium ravenspurgense
Clostridiales Family XIII bacterium
Corynebacterium pseudogenitalium
Eggerthella
Enterococcus faecalis
Escherichia
Facklamia hominis
Finegoldia magna
Gemella
Gleimia europaea
Hoylesella timonensis
Klebsiella
Peptoniphilus lacrimalis
Schaalia turicensis
Staphylococcus epidermidis
Staphylococcus hominis
Streptococcus
Ureaplasma
Ureaplasma parvum

Revision editor(s): Chloe, ChiomaBlessing, Tolulopeo, Chinelsy

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-22

Curated date: 2023/10/25

Curator: Tolulopeo

Revision editor(s): Tolulopeo, ChiomaBlessing

Differences from previous experiment shown

Subjects

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

Lab analysis

Statistical Analysis

Statistical test: LEfSe

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

Curated date: 2023/10/25

Curator: Tolulopeo

Revision editor(s): Tolulopeo, Chinelsy, ChiomaBlessing

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))

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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))

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Fannyhessea vaginae
Streptococcus infantis
Streptococcus mitis
Streptococcus oralis
Streptococcus pneumoniae

Revision editor(s): Tolulopeo, OdigiriGreat, ChiomaBlessing

Experiment 3