Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease/Experiment 5
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
- Distal colitis , Pancolitis distal colitis,inflammation of left colon,left colon inflammation,Distal colitis,pan-ulcerative colitis,pancolitis,universal colitis,Pancolitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- patients with proctitis ulcerative colitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients with left sided or extensive 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 defined as left sided (distal colitis) or extensive (pancolitis).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
- 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
- unchanged
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-26
Source: Figure 5c
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 left sided or extensive UC and proctitis.
Abundance in Group 1: increased abundance in patients with left sided or extensive ulcerative colitis
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium bifidum | ||
| Intestinibacter bartlettii | ||
| Flavonifractor plautii | ||
| Anaerostipes hadrus | ||
| Lacticaseibacillus paracasei | ||
| Mediterraneibacter gnavus |
Revision editor(s): Yjung24
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-26
Source: Figure 5c
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 left sided or extensive UC and proctitis.
Abundance in Group 1: decreased abundance in patients with left sided or extensive ulcerative colitis
