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
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
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 Control | Links |
|---|---|---|
| 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
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 Control | Links |
|---|---|---|
| Candidatus Gastranaerophilales |
Revision editor(s): Jeshudy
