Duodenal and rectal mucosal microbiota related to small intestinal bacterial overgrowth in diarrhea-predominant irritable bowel syndrome/Experiment 3
From BugSigDB
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
- 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 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
- rectal 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
- 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
