Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China
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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
Wu P, Zhang G, Zhao J, Chen J, Chen Y, Huang W, Zhong J, Zeng J
Journal
Frontiers in cellular and infection microbiology
Year
2018
Keywords:
extracellular matrix, inflammation, microbiota, urinary bladder neoplasms, urinary tract
Mounting evidence indicates that microbiome plays an important role in the development and progression of cancer. The dogma that urine in healthy individuals must be sterile has been overturned. Dysbiosis of the urinary microbiome has been revealed responsible for various urological disorders, including prostate cancer. The link between chronic inflammation, microbiome and solid tumors has been established for various neoplastic diseases. However, a detailed and comprehensive analysis of urinary microenvironment of bladder cancer has not been yet reported. We performed this study to characterize the potential urinary microbial community possibly associated with bladder cancer. Mid-stream urine was collected from 31 male patients with bladder cancer and 18 non-neoplastic controls. DNA was extracted from urine pellet samples and processed for high throughput 16S rRNA amplicon sequencing of the V4 region using Illumina MiSeq. Sequencing reads were filtered using QIIME and clustered using UPARSE. We observed increased bacterial richness (Observed Species, Chao 1 and Ace indexes; cancer vs. control; 120.0 vs. 56.0; 134.5 vs. 68.3; and 139.6 vs. 72.9, respectively), enrichment of some bacterial genera (e.g., Acinetobacter, Anaerococcus, and Sphingobacterium) and decrease of some bacterial genera (e.g., Serratia, Proteus, and Roseomonas) in cancer group when compared to non-cancer group. Significant difference in beta diversity was found between cancer and non-cancer group, among different risk level, but not among different tumor grade. Enrichment of Herbaspirillum, Porphyrobacter, and Bacteroides was observed in cancer patients with high risk of recurrence and progression, which means these genera maybe potential biomarkers for risk stratification. The PICRUSt showed that various functional pathways were enriched in cancer group, including Staphylococcus aureus infection, glycerolipid metabolism and retinol metabolism. To our knowledge, we performed the most comprehensive study to date to characterize the urinary microbiome associated with bladder cancer. A better understanding of the role of microbiome in the development and progression of bladder cancer could pave a new way for exploring new therapeutic options and biomarkers.
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)
- Within one 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
- 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
- 2.00
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
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Figure 4 B.
Description: Microbial taxa associated with bladder cancer. (B) Association of specific microbiota taxa with cancer group and non-cancer group by linear discriminant analysis effect size (LEfSe). Red indicates taxa enriched in cancer group and green indicates taxa enriched in non-cancer group.
Abundance in Group 1: increased abundance in Bladder cancer
Revision editor(s): Ayibatari
Signature 2
Source: Figure 4 B.
Description: Microbial taxa associated with bladder cancer. (B) Association of specific microbiota taxa with cancer group and non-cancer group by linear discriminant analysis effect size (LEfSe). Red indicates taxa enriched in cancer group and green indicates taxa enriched in non-cancer group.
Abundance in Group 1: decreased abundance in Bladder cancer
Revision editor(s): Ayibatari
Experiment 2
Differences from previous experiment shown
Subjects
- 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 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
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Supplementary Figures 4B
Description: Image_4_Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China.
Abundance in Group 1: increased abundance in Higher risk of recurrence (HER)
Revision editor(s): Ayibatari
Signature 2
Source: Supplementary Figures 4B.
Description: Image_4_Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China.
Abundance in Group 1: decreased abundance in Higher risk of recurrence (HER)
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia/Shigella sp. |
Revision editor(s): Ayibatari
Experiment 3
Differences from previous experiment shown
Subjects
- 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 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
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Supplementary Figures 5B.
Description: Image_5_Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China.
Abundance in Group 1: increased abundance in Higher risk of progression (HEP)
Revision editor(s): Ayibatari
Signature 2
Source: Supplementary Figures 5B.
Description: Image_5_Profiling the Urinary Microbiota in Male Patients With Bladder Cancer in China.
Abundance in Group 1: decreased abundance in Higher risk of progression (HEP)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Bacilli | ||
| Lactobacillales | ||
| uncultured Corynebacterium sp. | ||
| Cyanobacteriota |
Revision editor(s): Ayibatari
Experiment 4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Papillary urothelial neoplasm of low malignant potential (PUNLMP)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low-grade papillary urothelial carcinoma (LG)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Experiment 5
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-grade papillary urothelial carcinoma (HG)
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
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
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
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