Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-15
Subjects
- Location of subjects
- Canada
- 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
- Cecum mucosa , Colonic mucosa , Mucosa of rectum , Ileal mucosa Caecum mucosa,Caecum mucosa of organ,Caecum mucous membrane,Caecum organ mucosa,Cecal mucosa,Cecum mucosa of organ,Cecum mucous membrane,Cecum organ mucosa,Intestinum crassum caecum mucosa,Intestinum crassum caecum mucosa of organ,Intestinum crassum caecum mucous membrane,Intestinum crassum caecum organ mucosa,Mucosa of caecum,Mucosa of cecum,Mucosa of intestinum crassum caecum,Mucosa of organ of caecum,Mucosa of organ of cecum,Mucosa of organ of intestinum crassum caecum,Mucous membrane of caecum,Mucous membrane of cecum,Mucous membrane of intestinum crassum caecum,Organ mucosa of caecum,Organ mucosa of cecum,Organ mucosa of intestinum crassum caecum,Cecum mucosa,cecum mucosa,Colon mucosa,Colon mucous membrane,Colonic mucosa,Colonic mucous membrane,Large bowel mucosa,Mucosa of colon,Mucosa of large bowel,colonic mucosa,Mucosa of organ of rectum,Mucous membrane of rectum,Organ mucosa of rectum,Rectal mucosa,Rectal mucous membrane,Rectum mucosa,Rectum mucosa of organ,Rectum mucous membrane,Rectum organ mucosa,Mucosa of rectum,mucosa of rectum,Ileal mucous membrane,Ileum mucosa,Ileum mucosa of organ,Ileum mucous membrane,Ileum organ mucosa,Mucosa of ileum,Mucosa of organ of ileum,Mucous membrane of ileum,Organ mucosa of ileum,Ileal mucosa,ileal mucosa
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Ulcerative colitis colitis ulcerative,Colitis, Ulcerative,Left-sided ulcerative (chronic) colitis,Left-sided ulcerative colitis,left-sided ulcerative colitis,Other ulcerative colitis,Other ulcerative colitis (disorder),UC - ulcerative colitis,ulcerative colitis,ulcerative colitis (disease),ulcerative colitis (disorder),Ulcerative colitis, unspecified,ULCERATVE COLITIS UNSPCF,Ulcerative colitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non-inflammatory bowel disease patients who were undergoing colonoscopy either for screening or for other gastrointestinal complaints unrelated to IBD
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- inflamed ulcerative colitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- biopsies collected from patients with ulcerative colitis at colonoscopy that were deemed as inflamed as per the clinical pathologist.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- Group 1 sample size Number of subjects in the case (exposed) group
- 26
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- N/A
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V6
- 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).
- relative abundances
- Statistical test
- Kruskall-Wallis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- 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
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- increased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-15
Source: Table 2
Description: Microbial Distribution of Taxa (Phylum and Genus) Found to Be Differentially Abundant According to Disease and Inflammatory State of Biopsy. ^aP = <0.05, ^bP = <0.01, ^cP = <0.001. Up and down arrows are comparisons to non-IBD.
Abundance in Group 1: increased abundance in inflamed ulcerative colitis
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Pseudomonas |
Revision editor(s): Yjung24
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-15
Source: Table 2
Description: Microbial Distribution of Taxa (Phylum and Genus) Found to Be Differentially Abundant According to Disease and Inflammatory State of Biopsy. ^aP = <0.05, ^bP = <0.01, ^cP = <0.001. Up and down arrows are comparisons to non-IBD.
Abundance in Group 1: decreased abundance in inflamed ulcerative colitis
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Alistipes | ||
| Parabacteroides |
Revision editor(s): Yjung24
