Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
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 Chronic granulomatous disease
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnoclostridium | ||
| Sellimonas | ||
| Thomasclavelia | ||
| Veillonella | ||
| uncultured Roseburia sp. | ||
| uncultured bacterium |
Revision editor(s): Ifyohondu
Signature 2
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 Chronic granulomatous disease
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy individuals
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Chronic granulomatous disease (CGD) patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- CGD patients without a history of IBD and only receiving prophylactic antimicrobials
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- N/A
Lab analysis
Statistical Analysis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Fig. 2G
Description: Comparison of microbiome signatures between patients with CGD (without a history of IBD) VS Healthy individuals using LEfSe
Abundance in Group 1: increased abundance in Chronic granulomatous disease (CGD) patients
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Roseburia sp. | ||
| uncultured bacterium |
Revision editor(s): ChiomaBlessing
Signature 2
Source: Fig. 2G
Description: Comparison of microbiome signatures between patients with CGD (without a history of IBD) VS Healthy individuals using LEfSe
Abundance in Group 1: decreased abundance in Chronic granulomatous disease (CGD) patients
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricicoccus | ||
| Lachnospira eligens | ||
| uncultured bacterium | ||
| uncultured Lachnospiraceae bacterium | ||
| Intestinimonas butyriciproducens | ||
| Roseburia hominis |
Revision editor(s): ChiomaBlessing
Signature 3
Source: Fig. 2G
Description: Comparison of microbiome signatures between patients with CGD (without a history of IBD) VS Healthy individuals using LEfSe
Abundance in Group 1: increased abundance in Chronic granulomatous disease (CGD) patients
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Roseburia sp. | ||
| uncultured bacterium |
Revision editor(s): ChiomaBlessing
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cohort Cohort,cohort
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- PIDTC Cohort (CGD without IBD)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- NIHCC Cohort (CGD without IBD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Chronic granulomatous disease (CGD) without a history of Inflammatory bowel disease (IBD) and not receiving any medications other than prophylactic antimicrobials.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- 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
Statistical Analysis
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
Curated date: 2024/03/18
Curator: Ifyohondu
Revision editor(s): ChiomaBlessing, Folakunmi, Ifyohondu
Source: Fig. 3C
Description: Comparison of microbiome signatures between patients with CGD (without a history of IBD) from NIHCC VS PIDTC cohorts using LEfSe
Abundance in Group 1: decreased abundance in NIHCC Cohort (CGD without IBD)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus |
Revision editor(s): ChiomaBlessing, Folakunmi, Ifyohondu
Signature 2
Curated date: 2024/03/18
Curator: Ifyohondu
Revision editor(s): ChiomaBlessing, Folakunmi, Ifyohondu
Source: Fig. 3C
Description: Comparison of microbiome signatures between patients with CGD (without a history of IBD) from NIHCC VS PIDTC cohorts using LEfSe
Abundance in Group 1: increased abundance in NIHCC Cohort (CGD without IBD)
Revision editor(s): ChiomaBlessing, Folakunmi, Ifyohondu
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- PIDTC Cohort (CGD Patients)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- NIHCC Cohort (CGD Patients)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Chronic granulomatous disease (CGD) regardless of IBD status or antimicrobial use
- Group 0 sample size Number of subjects in the control (unexposed) group
- 36
- Group 1 sample size Number of subjects in the case (exposed) group
- 79
- 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
Statistical Analysis
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
Curated date: 2024/03/19
Curator: Ifyohondu
Revision editor(s): ChiomaBlessing, Folakunmi, Ifyohondu
Source: Fig E4C
Description: Comparison of microbiome signatures between patients with CGD (regardless of IBD status) from NIHCC VS PIDTC cohorts using LEfSe
Abundance in Group 1: decreased abundance in NIHCC Cohort (CGD Patients)
| NCBI | Quality Control | Links |
|---|---|---|
| Butyricicoccus | ||
| Streptococcus |
Revision editor(s): ChiomaBlessing, Folakunmi, Ifyohondu
Signature 2
Curated date: 2024/03/19
Curator: Ifyohondu
Revision editor(s): ChiomaBlessing, Folakunmi, Ifyohondu
Source: Fig E4C
Description: Comparison of microbiome signatures between patients with CGD (regardless of IBD status) from NIHCC VS PIDTC cohorts using LEfSe
Abundance in Group 1: increased abundance in NIHCC Cohort (CGD Patients)
Revision editor(s): ChiomaBlessing, Folakunmi, Ifyohondu
Experiment 6
Subjects
- 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
Lab analysis
Statistical Analysis
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
Curated date: 2024/03/19
Curator: Ifyohondu
Revision editor(s): ChiomaBlessing, Folakunmi, Ifyohondu
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): ChiomaBlessing, Folakunmi, Ifyohondu
