Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
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
- Urine Urine,urine
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Bladder carcinoma bladder cancer,bladder carcinoma,cancer of bladder,cancer of the bladder,cancer of the urinary bladder,cancer of urinary bladder,carcinoma bladder,carcinoma of bladder,carcinoma of the bladder,carcinoma of the urinary bladder,carcinoma of urinary bladder,urinary bladder cancer,urinary bladder carcinoma,Bladder carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-neoplastic (controls)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Bladder cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Male patients with bladder cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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)?
- 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
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 4B
Description: Microbial taxa associated with bladder cancer (red) versus non-cancer group (green)
Abundance in Group 1: increased abundance in Bladder cancer
Revision editor(s): Ayibatari, Scholastica
Signature 2
Source: Figure 4B
Description: Microbial taxa associated with bladder cancer (red) versus non-cancer group (green)
Abundance in Group 1: decreased abundance in Bladder cancer
NCBI | Quality Control | Links |
---|---|---|
Acetobacteraceae | ||
Bacteroidia | ||
Burkholderiaceae | ||
Eubacterium xylanophilum | ||
Proteus | ||
Rhodospirillales | ||
Roseomonas | ||
Serratia | ||
Ruminiclostridium-6Ruminiclostridium-6 | ||
Muribaculaceae |
Revision editor(s): Ayibatari, Scholastica
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Disease recurrence relapse,Disease recurrence,disease recurrence
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lower risk of recurrence (LER)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Higher risk of recurrence (HER)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Male bladder cancer patients stratified into the higher risk of recurrence group (HER, recurrence score of EORTC ≥ 5) based on European Organization for Research and Treatment of Cancer (EORTC) scoring system
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Supplementary Figure 4B
Description: Microbial taxa associated with high risk of recurrence (HER, red) versus low risk of recurrence (LER, green)
Abundance in Group 1: increased abundance in Higher risk of recurrence (HER)
Revision editor(s): Ayibatari, Scholastica
Signature 2
Source: Supplementary Figure 4B
Description: Microbial taxa associated with high risk of recurrence (HER, red) versus low risk of recurrence (LER, green)
Abundance in Group 1: decreased abundance in Higher risk of recurrence (HER)
NCBI | Quality Control | Links |
---|---|---|
Escherichia/Shigella sp. |
Revision editor(s): Ayibatari, Scholastica
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Disease progression measurement Disease progression measurement,disease progression measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lower risk of progression (LEP)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Higher risk of progression (HEP)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Male bladder cancer patients stratified into the higher risk of progression group (HEP, progression score of EORTC ≥ 7) based on European Organization for Research and Treatment of Cancer (EORTC) scoring system
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Supplementary Figure 5B
Description: Microbial taxa associated with high risk of progression (HEP, red) versus low risk of progression (LEP, green)
Abundance in Group 1: increased abundance in Higher risk of progression (HEP)
Revision editor(s): Ayibatari, Scholastica
Signature 2
Source: Supplementary Figure 5B
Description: Microbial taxa associated with high risk of progression (HEP, red) versus low risk of progression (LEP, green)
Abundance in Group 1: decreased abundance in Higher risk of progression (HEP)
NCBI | Quality Control | Links |
---|---|---|
Bacilli | ||
Bacillota | ||
Cyanobacteriota | ||
Lactobacillales | ||
uncultured Corynebacterium sp. |
Revision editor(s): Ayibatari, Scholastica