Diagnosis of Crohn's disease and ulcerative colitis using the microbiome/Experiment 6
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-4-1
Subjects
- Location of subjects
- South Korea
- 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
- 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
- Health controls (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ulcerative colitis disease patients- Mild, moderate and severe groups
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Ulcerative colitis disease in the mild, moderate and severe groups according to disease activity
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None.
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- MGISEQ-2000
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- T-Test
- 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
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-4-1
Source: Figure 3J
Description: Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- mild, moderate and severe groups compared to Healthy controls (HC)
Abundance in Group 1: decreased abundance in Ulcerative colitis disease patients- Mild, moderate and severe groups
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Porphyromonas asaccharolytica | ||
| Alistipes shahii |
Revision editor(s): ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-4-1
Source: Figure 3J
Description: Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC)- mild, moderate and severe groups compared to Healthy controls (HC)
Abundance in Group 1: increased abundance in Ulcerative colitis disease patients- Mild, moderate and severe groups
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Pantoea carbekii |
Revision editor(s): ChiomaBlessing
