A prospective study to examine the association of the urinary and fecal microbiota with prostate cancer diagnosis after transrectal biopsy of the prostate using 16sRNA gene analysis

Study information

Needs review

study design

prospective cohort

Citation

PMID PubMed identifier for scientific articles.

30117171

DOI Digital object identifier for electronic documents.

10.1002/pros.23713

URI Uniform resource identifier for web resources.

Authors

Alanee S, El-Zawahry A, Dynda D, Dabaja A, McVary K, Karr M, Braundmeier-Fleming A

Journal

The Prostate

Year

2019

INTRODUCTION: There is accumulating evidence that variations in the human microbiota may promote disease states including cancer. Our goal was to examine the association between urinary and fecal microbial profiles and the diagnosis of prostate cancer (PC) in patients undergoing transrectal biopsy of the prostate. MATERIALS AND METHODS: We extracted total DNA from urine and fecal samples collected before a prostate biopsy performed for elevated prostatic specific antigen in patients suspected of having PC. We then amplified the extracted DNA and sequenced it using bacterial 16S rRNA gene high-throughput next-generation sequencing platform, and analyzed microbial profiles for taxonomy comparing those patients diagnosed with PC with those who did not receive that diagnosis. RESULTS: We included 30 patients in our analysis (60 samples, one urine and one fecal per patient). The majority of patients with PC (10/14) had similar bacterial communities within their urinary sample profile and clustered separately than patients without cancer (n = 16). Differential analysis of the operational taxonomical units (OTUs) in urine samples revealed decreased abundance of several bacterial species in patients with prostate cancer. Analysis of the bacterial taxonomies of the fecal samples did not reveal any clustering in concordance with benign or malignant prostate biopsies. Patients who had a Gleason score (GS) of 6 (n = 11) were present in both urine bacterial community clusters, but patients with GS 7 or higher (n = 3) did not cluster tightly with non-cancer subjects. CONCLUSIONS: The urinary microbiota of patients with PC tends to cluster separately from those without this disease. Further research is needed to investigate the urinary microbiome potential of serving as a biomarker that could be used to improve the accuracy of pre-biopsy models predicting the presence of PC in post-biopsy tissue examination.

Experiment 1

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Curated date: 2021/01/10

Curator: WikiWorks743

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Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled (if applicable): Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Urine Urine

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: prostate cancer cancer of prostate gland,hereditary prostate cancer,malignant neoplasm of prostate,malignant neoplasm of prostate gland,malignant neoplasm of the prostate,malignant prostate gland neoplasm,malignant prostate neoplasm,malignant prostate tumor,malignant tumor of prostate,malignant tumor of the prostate,NGP - new growth of prostate,prostate cancer,prostate cancer, familial,prostate gland cancer,prostate neoplasm,prostatic cancer,prostatic neoplasm,tumor of the prostate

Group 0 name Corresponds to the control (unexposed) group for case-control studies: controls
Group 1 name Corresponds to the case (exposed) group for case-control studies: prostate cancer patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: the association of urinary and fecal microbiota with prostate cancer diagnosis
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: 14
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 28 days

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V5

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: Kruskall-Wallis

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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Signature 1

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Curated date: 2020-01-08

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743

Source: Table 1, Text

Description: Significant differential OTU frequencies in urine samples of patients with or without prostate cancer

Abundance in Group 1: increased abundance in prostate cancer patients

NCBI	Links
Bacteroides

Revision editor(s): WikiWorks743

Experiment 2

Edit History Delete

Mark reviewed

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled (if applicable): Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: prostate cancer cancer of prostate gland,hereditary prostate cancer,malignant neoplasm of prostate,malignant neoplasm of prostate gland,malignant neoplasm of the prostate,malignant prostate gland neoplasm,malignant prostate neoplasm,malignant prostate tumor,malignant tumor of prostate,malignant tumor of the prostate,NGP - new growth of prostate,prostate cancer,prostate cancer, familial,prostate gland cancer,prostate neoplasm,prostatic cancer,prostatic neoplasm,tumor of the prostate

Group 0 name Corresponds to the control (unexposed) group for case-control studies: controls
Group 1 name Corresponds to the case (exposed) group for case-control studies: prostate cancer patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: the association of urinary and fecal microbiota with prostate cancer diagnosis
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: 14
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 28 days

Lab analysis

Sequencing type: 16S

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Statistical test: Kruskall-Wallis

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