Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-26
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
- Patients with mild ulcerative colitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with moderate to severe ulcerative colitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients diagnosed with ulcerative colitis (UC) from 3 different academic hospitals in Korea categorized as moderate to severe forms of UC. The severity of disease was assessed by the Mayo score for UC. Severity was estimated at the time of fecal sampling, and the average follow-up period was 8.0 ± 1.3 years.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 37
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Patients who used drugs can affect intestinal microbial community, such as probiotics and antibiotics, within a month were excluded.
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
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.0
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-26
Source: Figure 5a
Description: Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between moderate to severe and mild UC (A).
Abundance in Group 1: increased abundance in Patients with moderate to severe ulcerative colitis
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridioides difficile | ||
| Ligilactobacillus salivarius |
Revision editor(s): Yjung24
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-26
Source: Figure 5a
Description: Taxa list according to linear discriminate analysis values determined from comparisons according to disease severity and extent in ulcerative colitis (UC) patients. Comparisons between moderate to severe and mild UC (A).
Abundance in Group 1: decreased abundance in Patients with moderate to severe ulcerative colitis
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides acidifaciens | ||
| Bacteroides caccae | ||
| Bilophila wadsworthia | ||
| Howardella ureilytica | ||
| Ruminococcus callidus | ||
| Streptococcus pneumoniae | ||
| [Clostridium] innocuum | ||
| Alistipes |
