Diagnosis of Crohn's disease and ulcerative colitis using the microbiome/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-23
Curated date: 2024/03/09
Curator: Samreen-19
Revision editor(s): ChiomaBlessing, Victoria, Samreen-19
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
- Healthy controls (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ulcerative colitis (UC) patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with ulcerative colitis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
- Group 1 sample size Number of subjects in the case (exposed) group
- 198
- 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).
- raw counts
- Statistical test
- Linear Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.0001
- 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 2024-3-23
Source: Supplemental. file: Table S8
Description: Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC) compared to healthy controls (HC)
Abundance in Group 1: increased abundance in Ulcerative colitis (UC) patients
Revision editor(s): Samreen-19, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-23
Source: Supplemental. file: Table S8
Description: Differences in the taxonomic composition of the gut microbiome in patients with Ulcerative colitis disease (UC) compared to healthy controls (HC)
Abundance in Group 1: decreased abundance in Ulcerative colitis (UC) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes shahii | ||
| Desulfovibrio sp. G11 | ||
| Victivallales bacterium CCUG 44730 | ||
| Odoribacter splanchnicus | ||
| Bradyrhizobium sp. ORS 278 | ||
| Akkermansia muciniphila |
Revision editor(s): Samreen-19, ChiomaBlessing
