Gut microbiome signatures reflect different subtypes of irritable bowel syndrome/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-6
Subjects
- Location of subjects
- United Kingdom
- United States of America
- 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
- 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
- Irritable bowel syndrome [X]Psychogenic IBS,Adaptive colitis,Colitides, Mucous,Colitis, Mucous,Colon spasm,Colon, Irritable,Functional bowel disease,IBD,IBS,IBS - Irritable bowel syndrome,IC - Irritable colon,Irritable bowel,Irritable bowel - IBS,irritable bowel syndrome,Irritable Bowel Syndromes,Irritable Colon,irritable colon,Irritable colon (disorder),Irritable colon - Irritable bowel syndrome,Irritable colon syndrome,Membranous colitis,Mucous Colitides,Mucous colitis,mucus colitis,Nervous colitis,Psychogenic IBS,psychogenic IBS,Spastic colitis,Spastic colon,spastic colon,Syndrome, Irritable Bowel,Syndromes, Irritable Bowel,Irritable bowel syndrome
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-IBS2 (Non-irritable bowel syndrome 2)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS-D (IBS-Diarrhea)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with IBS-D, a subtype of IBS characterized by diarrhea (watery stool)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 302
- Group 1 sample size Number of subjects in the case (exposed) group
- 302
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
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
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- age, alcohol drinking, body mass index, diet, geographic area, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, alcohol drinking, diet, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-5
Source: Figure 2a, b and c and Supplemental. Table 4
Description: Differential microbial abundance between IBS-D and Non-IBS2
Abundance in Group 1: decreased abundance in IBS-D (IBS-Diarrhea)
Revision editor(s): ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-5
Curated date: 2023/10/26
Curator: ChiomaBlessing
Revision editor(s): ChiomaBlessing, Iram jamshed, Folakunmi
Source: Figure 2a, b and c and Supplemental Table 4
Description: Differential microbial abundance between IBS-D and Non-IBS2
Abundance in Group 1: increased abundance in IBS-D (IBS-Diarrhea)
Revision editor(s): ChiomaBlessing, Iram jamshed, Folakunmi
