Duodenal and rectal mucosal microbiota related to small intestinal bacterial overgrowth in diarrhea-predominant 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
- China
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Small intestine Anterior intestine,Intestinum tenue,Mid intestine,Small bowel,Small intestine
- 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
- IBS.sibo-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS.sibo+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- typical clinical symptoms and normal colonoscopy presentation fulfilling the Rome III diagnostic criteria with SIBO
- Group 0 sample size Number of subjects in the control (unexposed) group
- 33
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months; also includes probiotics and proton-pump inhibitors
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 1
Source: Figure S3
Description: Enriched genera in duodenal mucosa obtained from LEfSe.
Abundance in Group 1: increased abundance in IBS.sibo+
NCBI | Quality Control | Links |
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Arthrobacter | ||
Carnobacterium | ||
Leuconostoc | ||
Bradyrhizobium | ||
Nevskia | ||
Lactococcus | ||
Pseudomonas |
Revision editor(s): Jeshudy
Signature 2
Source: Figure S3B
Description: Enriched genera in duodenal mucosa obtained from LEfSe.
Abundance in Group 1: decreased abundance in IBS.sibo+
Revision editor(s): Jeshudy
Experiment 2
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Duodenal mucosa Doudenal mucosa,Duodenal mucous membrane,Duodenum mucosa,Mucosa of duodenum,Mucous membrane of duodenum,Duodenal mucosa
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- small intestine enteropathy small bowel enteropathy,small intestine enteropathy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with typical clinical symptoms and normal colonoscopy presentation fulfilling the Rome III diagnostic criteria; with SIBO
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, body mass index
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
Experiment 3
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Mucosa of rectum Mucosa of organ of rectum,Mucous membrane of rectum,Organ mucosa of rectum,Rectal mucosa,Rectal mucous membrane,Rectum mucosa,Rectum mucosa of organ,Rectum mucous membrane,Rectum organ mucosa,Mucosa of rectum
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Experiment 4
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Duodenum Proximal intestine,Upper intestine,Duodenum
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HC.sibo-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HC.sibo+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy controls (no IBS) with SIBO
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
- Statistical test
- Chi-Square
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Table S1
Description: Comparisons of microbial composition at the phylum level between SIBO+ and SIBO- IBS-D patients and healthy individuals.
Abundance in Group 1: increased abundance in HC.sibo+
NCBI | Quality Control | Links |
---|---|---|
Bacteroidota |
Revision editor(s): Jeshudy
Experiment 5
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- IBS.sibo-
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS.sibo+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with typical clinical symptoms and normal colonoscopy presentation fulfilling the Rome III diagnostic criteria; with SIBO
- Group 0 sample size Number of subjects in the control (unexposed) group
- 33
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Source: Table S1
Description: Comparisons of microbial composition at the phylum level between SIBO+ and SIBO- IBS-D patients and healthy individuals.
Abundance in Group 1: increased abundance in IBS.sibo+
NCBI | Quality Control | Links |
---|---|---|
Bacillota |
Revision editor(s): Jeshudy