Differential Microbial Signature Associated With Benign Prostatic Hyperplasia and Prostate Cancer
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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
Sarkar P, Malik S, Banerjee A, Datta C, Pal DK, Ghosh A, Saha A
Journal
Frontiers in cellular and infection microbiology
Year
2022
Keywords:
EBV, HPV, benign prostate hyperplasia, microbiome, prostate cancer
Apart from other risk factors, chronic inflammation is also associated with the onset of Prostate Cancer (PCa), wherein pathogen infection and tissue microbiome dysbiosis are known to play a major role in both inflammatory response and cancer development. However, except for a few studies, the link between microbes and PCa remained poorly understood. To explore the potential microbiome signature associated with PCa in Indian patients, we investigated differential compositions of commensal bacteria among patients with benign prostatic hyperplasia (BPH) and PCa using 16S rRNA amplicon sequencing followed by qPCR analyses using two distinct primer sets. Using two independent cohorts, we show that Prevotella copri, Cupriavidus campinensis, and Propionibacterium acnes represent the three most abundant bacteria in diseased prostate lesions. LEfSe analyses identified that while Cupriavidus taiwanensis and Methylobacterium organophilum are distinctly elevated in PCa samples, Kocuria palustris and Cellvibrio mixtus are significantly enriched in BPH samples. Furthermore, we identify that a number of human tumor viruses, including Epstein-Barr virus (EBV) and hepatitis B virus (HBV), along with two high-risk human papillomaviruses - HPV-16 and HPV-18, are significantly associated with the PCa development and strongly correlated with PCa bacterial signature. The study may thus offer to develop a framework for exploiting this microbial signature for early diagnosis and prognosis of PCa development.
Experiment 1
Subjects
- Location of subjects
- India
- 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
- Prostate gland Male prostate,Prostata,Prostate,Prostate gland,prostate gland
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Prostate carcinoma cancer of prostate,cancer of the prostate,carcinoma of prostate,carcinoma of prostate gland,carcinoma of the prostate,prostate cancer,prostate cancer, NOS,prostate carcinoma,prostate gland carcinoma,Prostate carcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Benign prostatic hyperplasia (BPH), Cohort-1 (Discovery Cohort)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prostate Cancer (PCa), Cohort-1 (Discovery Cohort)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who are diagnosed with Prostate Cancer (PCa).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 33
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V2-V8
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
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
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Supplementary Figure 1E.
Description: Image_1_Differential Microbial Signature Associated With Benign Prostatic Hyperplasia and Prostate Cancer.
Abundance in Group 1: increased abundance in Prostate Cancer (PCa), Cohort-1 (Discovery Cohort)
| NCBI | Quality Control | Links |
|---|---|---|
| Bradyrhizobium |
Revision editor(s): Ayibatari
Signature 2
Source: Supplementary Figure 1E.
Description: Image_1_Differential Microbial Signature Associated With Benign Prostatic Hyperplasia and Prostate Cancer.
Abundance in Group 1: increased abundance in Prostate Cancer (PCa), Cohort-1 (Discovery Cohort)
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
- Benign prostatic hyperplasia (BPH), Cohort-2 (Validation Cohort)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Prostate Cancer (PCa), Cohort-2 (Validation Cohort)
- 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
- 16
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V9
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
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: FIGURE 2 D.
Description: Association of specific microbiota taxa (top 20 bacterial species) with BPH and PCa samples by LEfSe analyses. Green indicates taxa enriched in PCa samples.
Abundance in Group 1: increased abundance in Prostate Cancer (PCa), Cohort-2 (Validation Cohort)
Revision editor(s): Ayibatari
Signature 2
Source: FIGURE 2 D.
Description: Association of specific microbiota taxa (top 20 bacterial species) with BPH and PCa samples by LEfSe analyses. Orange indicates taxa enriched in BPH samples.
Abundance in Group 1: increased abundance in Prostate Cancer (PCa), Cohort-2 (Validation Cohort)
Revision editor(s): Ayibatari
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