Duodenal and rectal mucosal microbiota related to small intestinal bacterial overgrowth in diarrhea-predominant irritable bowel syndrome
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Yang M, Zhang L, Hong G, Li Y, Li G, Qian W, Xiong H, Bai T, Song J, Hou X
Journal
Journal of gastroenterology and hepatology
Year
2020
Keywords:
glucose hydrogen breath test, irritable bowel syndrome, microbial dysbiosis index, mucosal-associated microbiota, small intestinal bacterial overgrowth
BACKGROUND AND AIM: Small intestinal bacterial overgrowth (SIBO) has been proposed as an etiologic factor in irritable bowel syndrome, particularly the diarrhea-predominant subtype (IBS-D). We aimed to identify potential intestinal microbial pattern in IBS-D patients with SIBO. METHODS: Diarrhea-predominant irritable bowel syndrome patients fulfilling Rome III criteria were recruited and randomly divided into an exploratory cohort (57 cases) and a validation cohort (20 cases). SIBO was identified according to standard glucose hydrogen breath test. For 16S rRNA gene sequencing, samples of duodenal mucosa, duodenal fluid, rectal mucosa, and fresh feces were collected and performed. The α and β diversity, as well as differences in microbial composition and function, in SIBO+ and SIBO- IBS-D subjects were evaluated. RESULTS: The microbial diversity and composition obviously differed between SIBO+ and SIBO- IBS-D in duodenal and rectal mucosa but not in duodenal fluid and fresh feces. For rectal mucosal microbiota, it displayed markedly reduced aerobe and Gram-negative bacteria and increased facultative anaerobe and Gram-positive bacteria, moreover, altered functions of microbial metabolism in SIBO+ IBS-D. Significantly higher rectal mucosa-related microbial dysbiosis index was observed in SIBO+ IBS-D, and a cut-off value at -0.37 had a sensitivity of 56.55% and specificity of 90.91% to identify the SIBO in IBS-D subjects. CONCLUSIONS: Mucosal microbiota, rather than luminal bacteria, has a more apparent dysbiosis in SIBO+ IBS-D patients relative to those without SIBO. Rectal mucosa-associated microbiota may act as a potential predictor of SIBO in IBS-D patients.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-8
Subjects
- Location of subjects
- China
- 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
- Duodenal mucosa Doudenal mucosa,Duodenal mucous membrane,Duodenum mucosa,Mucosa of duodenum,Mucous membrane of duodenum,Duodenal mucosa,duodenal mucosa
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Small intestine enteropathy small bowel enteropathy,Small intestine enteropathy,small intestine enteropathy
- 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
- duodenal mucosa samples of 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
- 43
- Group 1 sample size Number of subjects in the case (exposed) group
- 34
- 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
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-8
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 |
|---|---|---|
| Arthrobacter | ||
| Carnobacterium | ||
| Leuconostoc | ||
| Bradyrhizobium | ||
| Nevskia | ||
| Lactococcus | ||
| Pseudomonas |
Revision editor(s): Jeshudy
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-8
Source: Figure S3B
Description: Enriched genera in duodenal mucosa obtained from LEfSe.
Abundance in Group 1: decreased abundance in IBS.sibo+
Experiment 3
Reviewed Marked as Reviewed by Folakunmi on 2024-2-8
Differences from previous experiment shown
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,mucosa of rectum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Small intestine enteropathy small bowel enteropathy,Small intestine enteropathy,small intestine enteropathy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- rectal mucosa samples of 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, body mass index, sex
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-8
Source: figure 3B
Description: Differentially abundant taxa in rectal mucosa between SIBO- IBS-D patients and SIBO+ IBS-D patients.
Abundance in Group 1: increased abundance in IBS.sibo+
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerovibrio | ||
| Carnobacterium | ||
| Enterococcus | ||
| Modestobacter | ||
| T78T78 | ||
| SMB53SMB53 | ||
| Geobacillus | ||
| Bifidobacterium | ||
| Propionibacterium | ||
| Helcococcus |
Revision editor(s): Folakunmi
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-8
Source: figure 3B
Description: Differentially abundant taxa in rectal mucosa between SIBO- IBS-D patients and SIBO+ IBS-D patients.
Abundance in Group 1: decreased abundance in IBS.sibo+
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Roseburia | ||
| Ruminococcus | ||
| Blautia | ||
| Staphylococcus | ||
| Janibacter | ||
| Citrobacter | ||
| Odoribacter | ||
| Methylobacterium | ||
| Deinococcus | ||
| Agrobacterium | ||
| Sphingobacterium |
Revision editor(s): Folakunmi
Experiment 4
Reviewed Marked as Reviewed by Folakunmi on 2024-2-8
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Duodenum Proximal intestine,Upper intestine,Duodenum,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
- duodenal fluid samples of healthy controls (with 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
Reviewed Marked as Reviewed by Folakunmi on 2024-2-8
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
Reviewed Marked as Reviewed by Folakunmi on 2024-2-8
Differences from previous experiment shown
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,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
- Feces samples of 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
- 43
- Group 1 sample size Number of subjects in the case (exposed) group
- 34
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-8
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
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