Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans/Experiment 1

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Curated date: 2024/03/15

Curator: Fetlework

Revision editor(s): Fetlework

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

Colorectal mucosa Colorectal mucosa,colorectal mucosa

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Colorectal adenoma adenoma of large bowel,adenoma of large intestine,adenoma of the large bowel,adenoma of the large intestine,colorectal adenoma,colorectum adenoma,large bowel adenoma,large intestine adenoma,Colorectal adenoma

Group 0 name Corresponds to the control (unexposed) group for case-control studies

adenoma

Group 1 name Corresponds to the case (exposed) group for case-control studies

adenoma-free

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

individual with colorectal adenoma

Group 0 sample size Number of subjects in the control (unexposed) group

33

Group 1 sample size Number of subjects in the case (exposed) group

38

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

no patient were using antibiotics during the study. However one case and one control subject reported antibiotics use in the last months before colonoscopy.

Lab analysis

Sequencing type

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

-V2

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

Roche454

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

centered log-ratio

Statistical test

Kruskall-Wallis

Linear Regression

Mann-Whitney (Wilcoxon)

Pearson Correlation

T-Test

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.1

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

Yes

Alpha Diversity

Simpson Estimator of species richness and species evenness: more weight on species evenness

increased

Richness Number of species

increased