Duodenal and rectal mucosal microbiota related to small intestinal bacterial overgrowth in diarrhea-predominant irritable bowel syndrome/Experiment 1
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
- 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+
