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/Experiment 1

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Reviewed Marked as Reviewed by Atrayees on 2023-6-26

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Subjects

Location of subjects
United States of America
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
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,Prostate cancer
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

Reviewed Marked as Reviewed by Atrayees on 2023-6-26

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks, Atrayees

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 Quality ControlLinks
Bacteroides

Revision editor(s): WikiWorks, Atrayees

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-26

Curated date: 2023/06/26

Curator: Atrayees

Revision editor(s): Atrayees

Source: Table 1, text

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

Abundance in Group 1: decreased abundance in prostate cancer patients

NCBI Quality ControlLinks
Faecalibacterium
Lachnospira
Acetanaerobacterium

Revision editor(s): Atrayees