Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease/Experiment 6
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-5-6
Subjects
- Location of subjects
- Canada
- 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
- Age Age,age
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- CGD patients less than or equal to 12 years
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- CGD patients above 12 years
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- CGD patients above 12 years old with no active IBD or history of IBD
- Group 0 sample size Number of subjects in the control (unexposed) group
- 26
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Recent treatment with non prophylactic antibiotics (acute antibiotics)
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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-4-9
Curated date: 2024/03/19
Curator: Ifyohondu
Revision editor(s): Ifyohondu, Folakunmi, ChiomaBlessing
Source: Fig E5D
Description: Effect of age on microbiome signatures in CGD patients (with no active IBD or history of IBD) comparing participants less than or equal to 12 years VS above 12 years using LEfSe
Abundance in Group 1: increased abundance in CGD patients above 12 years
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Bilophila | ||
| Butyricicoccus | ||
| Lachnospiraceae bacterium NK4A136 | ||
| Oscillibacter | ||
| Sellimonas | ||
| Subdoligranulum | ||
| [Ruminococcus] torques |
Revision editor(s): Ifyohondu, Folakunmi, ChiomaBlessing
