The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma/Experiment 2

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Reviewed Marked as Reviewed by Atrayees on 2023-7-17

Curated date: 2022/07/31

Curator: Jeshudy

Revision editor(s): Jeshudy, WikiWorks, Atrayees

Subjects

Location of subjects

Netherlands

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

Intestine Bowel,Intestinal tract,Intestine,intestine

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

non-adenoma group

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

adenoma group

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

Patients with a successful polypectomy. A total of 9 patients had advanced adenomas and 10 patients had non-advanced adenoma (NA), with a median size of the largest adenoma being 0.7 cm [IQR 0.5–0.8].

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

19

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

19

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

3 months prior to study inclusion and 3 months prior to second sample

Lab analysis

Sequencing type

16S

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

V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

Illumina

Statistical Analysis

Statistical test

LEfSe

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

0.05

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

2

Matched on Factors on which subjects have been matched on in a case-control study

smoking status, age, body mass index

Alpha Diversity

Richness Number of species

unchanged