Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states/Experiment 1
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
- No Growth
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Culture Positive
- 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
- 51
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "medication" 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.medication
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
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia coli | ||
| Klebsiella oxytoca | ||
| 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
| NCBI | Quality Control | Links |
|---|---|---|
| Ascomycota | ||
| Cutibacterium acnes |
