Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease/Experiment 1
From BugSigDB
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
- Chronic granulomatous disease Bridges-Good syndrome,CGD,chronic granulomatous disease,Chronic septic granulomatosis,chronic septic granulomatosis,congenital dysphagocytosis,granulomatous disease, chronic,Quie syndrome,Chronic granulomatous disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chronic granulomatous disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Chronic granulomatous disease and only receiving prophylactic antimicrobials and without a history of inflammatory bowel disease at the time of stool collection
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Recent treatment with nonprophylactic 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
- 2.5
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- inflammatory bowel disease, antibiotic, antimicrobial agent
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 Folakunmi on 2024-4-9
Source: Fig 2
Description: Difference between the intestinal microbiome of patients with Chronic granulomatous disease and healthy controls by LEfSe.
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnoclostridium | ||
| Sellimonas | ||
| Thomasclavelia | ||
| Veillonella | ||
| uncultured Roseburia sp. | ||
| uncultured bacterium |
Revision editor(s): Ifyohondu
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-4-9
Source: Fig 2
Description: Difference between the intestinal microbiome of patients with Chronic granulomatous disease and healthy controls by LEfSe .
Abundance in Group 1: decreased abundance in
