Gut microbiome signatures reflect different subtypes of irritable bowel syndrome/Experiment 4
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-6
Subjects
- Location of subjects
- Canada
- United Kingdom
- United States of America
- 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
- Depressive disorder depression,melancholia,melancholias,mental depression,syndrome, depressive,syndromes, depressive,Depressive disorder,depressive disorder
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- IBS patients without depression
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 134
- Group 1 sample size Number of subjects in the case (exposed) group
- 134
- 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
- MaAsLin2
- 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
- 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
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-5
Source: Figure 3C, Results (text)
Description: Differential microbial abundance between IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U) and IBS patients without depression
Abundance in Group 1: decreased abundance in IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Butyricimonas | ||
| Sutterella | ||
| Butyricicoccaceae |
Revision editor(s): ChiomaBlessing, Atrayees
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-5
Source: Figure 3C, Results (text)
Description: Differential microbial abundance between IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U) and IBS patients without depression
Abundance in Group 1: increased abundance in IBS patients with depression in all three subtypes (IBS-D, IBS-C and IBS-U)
| NCBI | Quality Control | Links |
|---|---|---|
| Proteus |
Revision editor(s): ChiomaBlessing
