Shifts in the Fecal Microbiota Associated with Adenomatous Polyps/Experiment 1
From BugSigDB
Needs review
Curated date: 2022/06/29
Curator: Jeshudy
Revision editor(s): WikiWorks, Jeshudy, Suwaiba, Peace Sandy
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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- 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 1 name Corresponds to the case (exposed) group for case-control studies
- Adenoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with colorectal adenoma as identified during a screening colonoscopy. Fecal samples from patients in which at least one adenoma > 1 cm was identified were included in the “adenoma” group.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 547
- Group 1 sample size Number of subjects in the case (exposed) group
- 233
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None specified
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
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- Linear Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.2
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2B
Description: −log(P value) of these taxa’s differential abundance.
Abundance in Group 1: increased abundance in Adenoma
| NCBI | Quality Control | Links |
|---|---|---|
| Alcaligenaceae | ||
| Bacteroidales | ||
| Bacteroidota | ||
| Betaproteobacteria | ||
| Bilophila | ||
| Burkholderiales | ||
| Deltaproteobacteria | ||
| Mogibacterium | ||
| Sutterella |
Signature 2
Source: Figure 2B
Description: −log(P value) of these taxa’s differential abundance.
Abundance in Group 1: decreased abundance in Adenoma
