Profiling the urinary microbiome in men with calcium-based kidney stones/Experiment 2
From BugSigDB
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
- Renal pelvis/ureter Renal pelvis and ureter,Renal pelvis plus ureter,Renal pelvis/ureter,renal pelvis/ureter
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Nephrolithiasis Calculi, Kidney,Calculi, Renal,calculus of kidney and ureter,Calculus, Kidney,Calculus, Renal,CAON,Kidney Calculi,Kidney Calculus,kidney stone,Kidney Stones,Kidney stones,kidney stones,nephrolithiasis,nephrolithiasis, calcium oxalate,Renal Calculi,Renal calculi,renal calculi,Renal Calculus,Renal stones,Stone - kidney/ureter,Stone, Kidney,Stones, Kidney,urolithiasis, calcium oxalate,Nephrolithiasis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- KB group - Bladder urine from kidney stone patients.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- KP group - Renal pelvis urine from kidney stone patients.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Renal pelvis urine collected from nephrolithiasis (Kidney stone) patients.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Participants using antibiotics within 30days were excluded.
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
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Signature 1
Source: Fig. 5A & 5B
Description: A Cladogram and LEfSe analyses of microbiomes among HB (red), KB (green) and KP (blue) groups. Taxa in graph were with LDA score threshold > 2.0 and statistically significant (p < 0.05)
Abundance in Group 1: increased abundance in KP group - Renal pelvis urine from kidney stone patients.
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriaceae | ||
| Fusobacterium | ||
| Pseudomonadota | ||
| Gammaproteobacteria | ||
| Moraxellaceae | ||
| Acinetobacter | ||
| Pseudomonadales |
Revision editor(s): Victoria
Signature 2
Source: Fig. 5A & 5B
Description: A Cladogram and LEfSe analyses of microbiomes among HB (red), KB (green) and KP (blue) groups. Taxa in graph were with LDA score threshold > 2.0 and statistically significant (p < 0.05)
Abundance in Group 1: decreased abundance in KP group - Renal pelvis urine from kidney stone patients.
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetales | ||
| Anoxybacillus |
Revision editor(s): Victoria
