Profiling the urinary microbiome in men with calcium-based kidney stones
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Xie J, Huang JS, Huang XJ, Peng JM, Yu Z, Yuan YQ, Xiao KF, Guo JN
Journal
BMC microbiology
Year
2020
Keywords:
Calcium-based, Kidney stone, Microbiome, Renal pelvis, Urine
BACKGROUND: The dogma that urine is sterile in healthy individuals has been overturned by recent studies applying molecular-based methods. Mounting evidences indicate that dysbiosis of the urinary microbiota is associated with several urological diseases. In this study, we aimed to investigate the urinary microbiome of male patients with calcium-based kidney stones and compare it with those of healthy individuals. RESULTS: The diversity of the urinary microbiota in kidney stone patients was significantly lower than that of healthy controls based on the Shannon and Simpson index (P < 0.001 for both indices). The urinary microbiota structure also significantly differed between kidney stone patients and healthy controls (ANOSIM, R = 0.11, P < 0.001). Differential representation of inflammation associated bacteria (e.g., Acinetobacter) and several enriched functional pathways were identified in the urine of kidney stones patients. Meanwhile, we found the species diversity, overall composition of microbiota and predicted functional pathways were similar between bladder urine and renal pelvis urine in kidney stone patients. CONCLUSIONS: A marked dysbiosis of urinary microbiota in male patients with calcium-based kidney stones was observed, which may be helpful to interpret the association between bacteria and calcium-based kidney stones.
Experiment 1
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
- Urinary bladder Bladder,Urocyst,Vesica,Vesica urinaria,Urinary bladder,urinary bladder
- 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
- HB group - Bladder urine from healthy controls.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- KB group - Bladder urine from kidney stone patients.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Bladder urine collected from nephrolithiasis (Kidney stone) patients.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- 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)
- 30 days.
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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
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 KB group - Bladder urine from kidney stone patients.
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 KB group - Bladder urine from kidney stone patients.
| NCBI | Quality Control | Links |
|---|---|---|
| Moraxellaceae | ||
| Acinetobacter | ||
| Pseudomonadales | ||
| Gammaproteobacteria | ||
| Pseudomonadota | ||
| Fusobacterium | ||
| Fusobacteriaceae |
Revision editor(s): Victoria
Experiment 2
Differences from previous experiment shown
Subjects
- 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
- 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
- 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
Statistical Analysis
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
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