Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-3-13
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
- Insignificant Samples
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Culture Positive Samples
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with urine specimen with significant growth of 1–2 uropathogenic species at ≥10^5 colony forming units (CFU)/mL
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 48
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 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
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-3-13
Source: Fig 3 and Result Text (under "Diagnostic categories reflect different states of urobiome health, paragraph 2")
Description: Significantly enriched microbiota in suspected Urinary Tract Infection specimens from different clinical categories.
Abundance in Group 1: increased abundance in Culture Positive Samples
| NCBI | Quality Control | Links |
|---|---|---|
| Klebsiella pneumoniae |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-3-13
Source: Fig 3 and Result Text (under "Diagnostic categories reflect different states of urobiome health, paragraph 2")
Description: Significantly enriched microbiota in suspected Urinary Tract Infection specimens from different clinical categories.
Abundance in Group 1: decreased abundance in Culture Positive Samples
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides ovatus | ||
| [Ruminococcus] torques |
