Gut microbiome signatures reflect different subtypes of irritable bowel syndrome
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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
- 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-IBS1 (Non-irritable bowel syndrome 1)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS-C (IBS-Constipation)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with IBS-C, a subtype of IBS characterized by constipation (difficulty passing stool)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 180
- Group 1 sample size Number of subjects in the case (exposed) group
- 180
- 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
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2a, b and c and Supplemental. Table 3
Description: Differential microbial abundance between IBS-C and Non-IBS1
Abundance in Group 1: decreased abundance in IBS-C (IBS-Constipation)
Revision editor(s): ChiomaBlessing
Signature 2
Source: Figure 2a, b and c and Supplemental Table 3
Description: Differential microbial abundance between IBS-C and Non-IBS1
Abundance in Group 1: increased abundance in IBS-C (IBS-Constipation)
Revision editor(s): ChiomaBlessing, Folakunmi
Experiment 2
Subjects
- 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
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
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
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
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-IBS3 (Non-irritable bowel syndrome 3)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS-U (IBS-Unclassified)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with IBS-U, a distinct category characterized by normal formed stool
- Group 0 sample size Number of subjects in the control (unexposed) group
- 460
- Group 1 sample size Number of subjects in the case (exposed) group
- 460
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2a, b and c and Supplemental. Table 5
Description: Differential microbial abundance between IBS-U and Non-IBS3
Abundance in Group 1: decreased abundance in IBS-U (IBS-Unclassified)
Revision editor(s): ChiomaBlessing, Folakunmi
Signature 2
Source: IBS-U (IBS-Unclassified)
Description: Differential microbial abundance between IBS-U and Non-IBS3
Abundance in Group 1: increased abundance in IBS-U (IBS-Unclassified)
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia/Shigella sp. | ||
| Pseudomonas | ||
| Succiniclasticum | ||
| [Ruminococcus] torques | ||
| Pseudomonadota |
Revision editor(s): ChiomaBlessing, Folakunmi
Experiment 4
Subjects
- Location of subjects
- Canada
- United Kingdom
- United States of America
- 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
Lab analysis
Statistical Analysis
- Statistical test
- MaAsLin2
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
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
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
Experiment 5
Subjects
- Location of subjects
- United Kingdom
- United States of America
- Canada
- 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-IBS (Non-irritable bowel syndrome)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS-C (IBS-Constipation) Validation Cohort
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with IBS-C, a subtype of IBS characterized by constipation (difficulty passing stool) in the Validation Cohort
- Group 0 sample size Number of subjects in the control (unexposed) group
- 44
- Group 1 sample size Number of subjects in the case (exposed) group
- 44
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- 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
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Supplemental. Figure 5C
Description: Differential microbial abundance between IBS-C and Non-IBS (Validation cohort)
Abundance in Group 1: decreased abundance in IBS-C (IBS-Constipation) Validation Cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Actinomycetota |
Revision editor(s): ChiomaBlessing
Signature 2
Source: Supplemental Figure 5C
Description: Differential microbial abundance between IBS-C and Non-IBS (Validation cohort)
Abundance in Group 1: increased abundance in IBS-C (IBS-Constipation) Validation Cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Verrucomicrobiota |
Revision editor(s): ChiomaBlessing
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS-D (IBS-Diarrhea) Validation Cohort
- 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) in the Validation Cohort
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 48
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Supplemental Figure 5C
Description: Differential microbial abundance between IBS-D and Non-IBS (Validation cohort)
Abundance in Group 1: decreased abundance in IBS-D (IBS-Diarrhea) Validation Cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacillota | ||
| Campylobacterota |
Revision editor(s): ChiomaBlessing
Signature 2
Source: Supplemental Figure 5C
Description: Differential microbial abundance between IBS-D and Non-IBS (Validation cohort)
Abundance in Group 1: increased abundance in IBS-D (IBS-Diarrhea) Validation Cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota |
Revision editor(s): ChiomaBlessing
Experiment 7
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS-U (IBS-Unclassified) Validation Cohort
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with IBS-U, a distinct category characterized by normal formed stool in the Validation Cohort
- Group 0 sample size Number of subjects in the control (unexposed) group
- 61
- Group 1 sample size Number of subjects in the case (exposed) group
- 61
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Supplemental Figure 5C
Description: Differential microbial abundance between IBS-U and Non-IBS (Validation cohort)
Abundance in Group 1: decreased abundance in IBS-U (IBS-Unclassified) Validation Cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Actinomycetota |
Revision editor(s): ChiomaBlessing
Signature 2
Source: Supplemental Figure 5C
Description: Differential microbial abundance between IBS-U and Non-IBS (Validation cohort)
Abundance in Group 1: increased abundance in IBS-U (IBS-Unclassified) Validation Cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota |
Revision editor(s): ChiomaBlessing
