The potential of fecal microbiota and amino acids to detect and monitor patients with adenoma/Experiment 4

From BugSigDB


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

Curated date: 2022/07/31

Curator: Jeshudy

Revision editor(s): Jeshudy, WikiWorks

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
adenoma group pre-polypectomy
Group 1 name Corresponds to the case (exposed) group for case-control studies
adenoma group post-polypectomy
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
32
Group 1 sample size Number of subjects in the case (exposed) group
32
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
Matched on: "subject" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.subject


Signature 1

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

Curated date: 2022/07/31

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Figure 3

Description: Distribution of selected taxa for baseline versus follow-up.

Abundance in Group 1: increased abundance in adenoma group post-polypectomy

NCBI Quality ControlLinks
Anaerobutyricum hallii
unclassified Candidatus Izimaplasma
unclassified Enterobacteriaceae
unclassified Puniceicoccaceae
unclassified Clostridium

Revision editor(s): Jeshudy

Signature 2

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

Curated date: 2022/07/31

Curator: Jeshudy

Revision editor(s): Jeshudy

Source: Figure 2

Description: Distribution of selected taxa for adenomas at baseline and follow-up.

Abundance in Group 1: increased abundance in adenoma group post-polypectomy

NCBI Quality ControlLinks
Candidatus Gastranaerophilales

Revision editor(s): Jeshudy