Alternation of the gut microbiota in irritable bowel syndrome: an integrated analysis based on multicenter amplicon sequencing data
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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
- Australia
- Canada
- Switzerland
- United Kingdom
- 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
- 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
- Healthy Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS Patients (Irritable Bowel Syndrome)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group represents individuals diagnosed with irritable bowel syndrome (IBS), as identified from multicenter 16S rRNA sequencing data curated in the GMrepo database.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 354
- Group 1 sample size Number of subjects in the case (exposed) group
- 354
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, region, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, region, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Fig. 2b, c, d, S4, S5 & S6
Description: The relative abundance of the taxa between the IBS and healthy controls.
Abundance in Group 1: increased abundance in IBS Patients (Irritable Bowel Syndrome)
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Bacillota | ||
| Bacillus | ||
| Enterobacteriaceae | ||
| Enterocloster | ||
| Holdemania | ||
| Moraxellaceae | ||
| Sphingobacteriaceae | ||
| Sphingobacterium | ||
| Streptococcus |
Revision editor(s): Joiejoie
Signature 2
Source: Fig. 2b, c, d, S4, S5 & S6
Description: The relative abundance of the taxa between the IBS and healthy controls.
Abundance in Group 1: decreased abundance in IBS Patients (Irritable Bowel Syndrome)
Revision editor(s): Joiejoie
Experiment 2
Subjects
- 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
- IBS-C ( Irritable bowel syndrome with predominant constipation )
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to patients diagnosed with irritable bowel syndrome complicated with predominant constipation.
- Group 1 sample size Number of subjects in the case (exposed) group
- 79
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Fig. 4C
Description: Relative abundance of significantly enriched genera.
Abundance in Group 1: increased abundance in IBS-C ( Irritable bowel syndrome with predominant constipation )
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerofilum | ||
| Bacillus | ||
| Enterocloster | ||
| Holdemania | ||
| Sphingobacterium | ||
| Streptococcus |
Revision editor(s): Joiejoie
Signature 2
Source: Fig. 4C
Description: Relative abundance of significantly depleted genera.
Abundance in Group 1: decreased abundance in IBS-C ( Irritable bowel syndrome with predominant constipation )
Revision editor(s): Joiejoie
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS-D (Irritable bowel syndrome with predominant diarrhea )
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to patients diagnosed with irritable bowel syndrome complicated with predominant diarrhea.
- Group 1 sample size Number of subjects in the case (exposed) group
- 81
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Fig. 4C
Description: Relative abundance of significantly enriched genera.
Abundance in Group 1: increased abundance in IBS-D (Irritable bowel syndrome with predominant diarrhea )
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Sphingobacterium | ||
| Holdemania | ||
| Streptococcus | ||
| Bacillus | ||
| Peptoniphilus | ||
| Roseburia | ||
| Enterocloster |
Revision editor(s): Joiejoie
Signature 2
Source: Fig. 4C
Description: Relative abundance of significantly depleted genera.
Abundance in Group 1: decreased abundance in IBS-D (Irritable bowel syndrome with predominant diarrhea )
Revision editor(s): Joiejoie
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- IBS-C (Irritable bowel syndrome with predominant constipation)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This refers to patients diagnosed with irritable bowel syndrome complicated with predominant diarrhea.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 79
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Fig. 4C
Description: Relative abundance of significantly enriched genera.
Abundance in Group 1: increased abundance in IBS-D (Irritable bowel syndrome with predominant diarrhea )
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Corynebacterium | ||
| Prevotella | ||
| Faecalibacterium | ||
| Lachnospira | ||
| Streptococcus | ||
| Coprococcus | ||
| Peptoniphilus | ||
| Roseburia | ||
| Enterocloster |
Revision editor(s): Joiejoie
Signature 2
Source: Fig. 4C
Description: Relative abundance of significantly depleted genera
Abundance in Group 1: decreased abundance in IBS-D (Irritable bowel syndrome with predominant diarrhea )
| NCBI | Quality Control | Links |
|---|---|---|
| Bilophila | ||
| Barnesiella | ||
| Phocaeicola | ||
| Anaerofilum | ||
| Holdemania | ||
| Sarcina | ||
| Acidaminococcus | ||
| Oscillospiraceae incertae sedis | ||
| Bacillus | ||
| Oscillibacter | ||
| Sporobacter | ||
| Ruminococcus | ||
| Acetivibrio |
Revision editor(s): Joiejoie
Experiment 5
Subjects
- 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
- IBS-NPD ( Irritable Bowel Syndrome without psychiatric disorders )
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to patients with irritable bowel syndrome without psychiatric disorders (IBS-NPD)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 354
- Group 1 sample size Number of subjects in the case (exposed) group
- 214
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Fig. 5C
Description: The relative abundance of significantly enriched genera.
Abundance in Group 1: increased abundance in IBS-NPD ( Irritable Bowel Syndrome without psychiatric disorders )
| NCBI | Quality Control | Links |
|---|---|---|
| Sphingobacterium | ||
| Holdemania | ||
| Enterocloster | ||
| Niallia |
Revision editor(s): Joiejoie
Signature 2
Source: Fig. 5C
Description: The relative abundance of significantly depleted genera.
Abundance in Group 1: decreased abundance in IBS-NPD ( Irritable Bowel Syndrome without psychiatric disorders )
Revision editor(s): Joiejoie
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS-PD ( Irritable Bowel Syndrome with psychiatric disorders )
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to patients with irritable bowel syndrome with psychiatric disorders (IBS-PD)
- Group 1 sample size Number of subjects in the case (exposed) group
- 140
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Fig. 5C
Description: The relative abundance of significantly enriched genera.
Abundance in Group 1: increased abundance in IBS-PD ( Irritable Bowel Syndrome with psychiatric disorders )
| NCBI | Quality Control | Links |
|---|---|---|
| Sphingobacterium | ||
| Holdemania | ||
| Enterocloster | ||
| Pseudoflavonifractor |
Revision editor(s): Joiejoie
Signature 2
Source: Fig. 5C
Description: The relative abundance of significantly depleted genera.
Abundance in Group 1: decreased abundance in IBS-PD ( Irritable Bowel Syndrome with psychiatric disorders )
Revision editor(s): Joiejoie
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- IBS-NPD (Irritable Bowel Syndrome without psychiatric disorders)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS-PD (Irritable Bowel Syndrome with psychiatric disorders)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 214
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Fig. 5C
Description: The relative abundance of significantly enriched genera.
Abundance in Group 1: increased abundance in IBS-PD (Irritable Bowel Syndrome with psychiatric disorders)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Phocaeicola | ||
| Prevotella | ||
| Sphingobacterium | ||
| Faecalibacterium | ||
| Ruminococcus | ||
| Enterocloster | ||
| Pseudoflavonifractor | ||
| Butyrivibrio |
Revision editor(s): Joiejoie
Signature 2
Source: Fig. 5C
Description: The relative abundance of significantly depleted genera.
Abundance in Group 1: decreased abundance in IBS-PD (Irritable Bowel Syndrome with psychiatric disorders)
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcus | ||
| Niallia | ||
| Ruminiclostridium | ||
| Pseudoclostridium | ||
| Holdemania | ||
| Sarcina | ||
| Paraprevotella | ||
| Bilophila | ||
| Coprococcus | ||
| Sporobacter | ||
| Acetivibrio |
Revision editor(s): Joiejoie
Experiment 8
Subjects
- 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
- IBS Patients (Irritable Bowel Syndrome)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group represents individuals diagnosed with irritable bowel syndrome (IBS), as identified from multicenter 16S rRNA sequencing data curated in the GMrepo database.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 354
- Group 1 sample size Number of subjects in the case (exposed) group
- 354
Lab analysis
Statistical Analysis
- Statistical test
- Random Forest Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Fig. 7A & B
Description: The top-ranked biomarkers identified at the genus and species level to distinguish IBS from healthy controls on their mean decrease scores of the optimal model performance
Abundance in Group 1: increased abundance in IBS Patients (Irritable Bowel Syndrome)
Revision editor(s): Joiejoie
Signature 2
Source: Fig. 7A & B
Description: The top-ranked biomarkers identified at the genus and species level to distinguish IBS from healthy controls on their mean decrease scores of the optimal model performance
Abundance in Group 1: decreased abundance in IBS Patients (Irritable Bowel Syndrome)
Revision editor(s): Joiejoie
