Differential Microbial Signature Associated With Benign Prostatic Hyperplasia and Prostate Cancer

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Reviewed Marked as Reviewed by Svetlana up on 2024-6-12
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


Reviewed Marked as Reviewed by Svetlana up on 2024-6-12

Curated date: 2024/04/06

Curator: Ayibatari

Revision editor(s): Ayibatari, Scholastica

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
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
None

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V2-V9
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
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
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
decreased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-6-12

Curated date: 2024/04/06

Curator: Ayibatari

Revision editor(s): Ayibatari, Scholastica

Source: Fig 2D, Supp. Fig 1E

Description: Differential Microbial Signature Associated With Benign Prostatic Hyperplasia versus Prostate Cancer.

Abundance in Group 1: increased abundance in Prostate Cancer (PCa), Cohort-1 (Discovery Cohort)

NCBI Quality ControlLinks
Bradyrhizobium
Neisseria elongata
Leclercia adecarboxylata
Caulobacter segnis
Cupriavidus basilensis
Bradyrhizobium cytisi
Acinetobacter junii
Neisseria flavescens
Brevundimonas vancanneytii
Methylobacterium organophilum
Cupriavidus taiwanensis

Revision editor(s): Ayibatari, Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-6-12

Curated date: 2024/04/06

Curator: Ayibatari

Revision editor(s): Ayibatari, Scholastica

Source: Fig 2D, Supp. Fig 1E

Description: Differential Microbial Signature Associated With Benign Prostatic Hyperplasia versus Prostate Cancer.

Abundance in Group 1: increased abundance in Prostate Cancer (PCa), Cohort-1 (Discovery Cohort)

NCBI Quality ControlLinks
Aeromicrobium
Anaerococcus
Brachybacterium
Brevibacterium
Cellvibrio
Chryseobacterium
Comamonas
Corynebacterium
Empedobacter
Kocuria
Lysobacter
Microvirga
Paracoccus
Pseudomonas
Pseudoxanthomonas
Rhodobacter
Serinicoccus
Staphylococcus
Stenotrophomonas
Kocuria palustris
Cellvibrio mixtus
Stutzerimonas stutzeri
Paracoccus sp.Paracoccus sp.
Staphylococcus hominis
Corynebacterium tuberculostearicum
Brachybacterium paraconglomeratum
Staphylococcus arlettae
Staphylococcus cohnii
Anaerococcus octavius

Revision editor(s): Ayibatari, Scholastica