Differential Urinary Microbiota Composition Between Women With and Without Recurrent Urinary Tract Infection/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2023-10-17
Subjects
- Location of subjects
- China
- 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
- Asymptomatic controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Recurrent Urinary Tract Infection (RUTI) patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Women with clinically diagnosed RUTI with negative Standard Urine Cultures (SUCs)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 44
- Group 1 sample size Number of subjects in the case (exposed) group
- 67
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Patients with antibiotic treatment in the previous 48 hours (2 days) and their symptoms relieved.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
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
- 3
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2023-10-16
Source: Figure 5
Description: Differentially abundant bacteria between RUTI and controls, revealed by linear discriminant analysis effect size (LEfSe) analysis.
Abundance in Group 1: increased abundance in Recurrent Urinary Tract Infection (RUTI) patients
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2023-10-16
Source: Figure 5
Description: Differentially abundant bacteria between RUTI and controls, revealed by linear discriminant analysis effect size (LEfSe) analysis.
Abundance in Group 1: decreased abundance in Recurrent Urinary Tract Infection (RUTI) patients
