Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states/Experiment 2

From BugSigDB


Reviewed Marked as Reviewed by Folakunmi on 2024-3-13

Curated date: 2024/03/06

Curator: MyleeeA

Revision editor(s): MyleeeA

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

Curated date: 2024/03/06

Curator: MyleeeA

Revision editor(s): MyleeeA, Folakunmi

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 ControlLinks
Klebsiella pneumoniae

Revision editor(s): MyleeeA, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-3-13

Curated date: 2024/03/06

Curator: MyleeeA

Revision editor(s): MyleeeA, Folakunmi

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 ControlLinks
Bacteroides ovatus
[Ruminococcus] torques

Revision editor(s): MyleeeA, Folakunmi