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 States of America
- United Kingdom
- Australia
- 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
- 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
- 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, Matched on: "gender" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.gender
- 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
Experiment 2
Subjects
- Location of subjects
- Australia
- United Kingdom
- United States of America
- 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
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)
| NCBI | Quality Control | Links |
|---|---|---|
| Abiotrophia | ||
| Dorea | ||
| Escherichia/Shigella sp. | ||
| Flavonifractor | ||
| Haemophilus | ||
| Subdoligranulum | ||
| [Ruminococcus] gnavus | ||
| Defluviitaleaceae |
Revision editor(s): ChiomaBlessing, Iram jamshed
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
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 |
Revision editor(s): ChiomaBlessing
Experiment 4
Subjects
- 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
- 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
- Linear Regression
- 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_UCG_009Butyricicoccaceae_UCG_009 |
Revision editor(s): ChiomaBlessing
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
- 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
- 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
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
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
