Molecular analysis of the luminal- and mucosal-associated intestinal microbiota in diarrhea-predominant irritable bowel syndrome

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-28
study design
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Carroll IM, Ringel-Kulka T, Keku TO, Chang YH, Packey CD, Sartor RB, Ringel Y
American journal of physiology. Gastrointestinal and liver physiology
Alterations in the intestinal microbiota have been suggested as an etiological factor in the pathogenesis of irritable bowel syndrome (IBS). This study used a molecular fingerprinting technique to compare the composition and biodiversity of the microbiota within fecal and mucosal niches between patients with diarrhea-predominant IBS (D-IBS) and healthy controls. Terminal-restriction fragment (T-RF) length polymorphism (T-RFLP) fingerprinting of the bacterial 16S rRNA gene was used to perform microbial community composition analyses on fecal and mucosal samples from patients with D-IBS (n = 16) and healthy controls (n = 21). Molecular fingerprinting of the microbiota from fecal and colonic mucosal samples revealed differences in the contribution of T-RFs to the microbiota between D-IBS patients and healthy controls. Further analysis revealed a significantly lower (1.2-fold) biodiversity of microbes within fecal samples from D-IBS patients than healthy controls (P = 0.008). No difference in biodiversity in mucosal samples was detected between D-IBS patients and healthy controls. Multivariate analysis of T-RFLP profiles demonstrated distinct microbial communities between luminal and mucosal niches in all samples. Our findings of compositional differences in the luminal- and mucosal-associated microbiota between D-IBS patients and healthy controls and diminished microbial biodiversity in D-IBS fecal samples further support the hypothesis that alterations in the intestinal microbiota may have an etiological role in the pathogenesis of D-IBS and suggest that luminal and mucosal niches need to be investigated.

Experiment 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-28

Curated date: 2022/01/19

Curator: Kwekuamoo

Revision editor(s): WikiWorks, Kwekuamoo, Atrayees, Aiyshaaaa, Peace Sandy


Location of subjects
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 , Colonic mucosa 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,Colon mucosa,Colon mucous membrane,Colonic mucosa,Colonic mucous membrane,Large bowel mucosa,Mucosa of colon,Mucosa of large bowel,colonic mucosa
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 Control
Group 1 name Corresponds to the case (exposed) group for case-control studies
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Individual who have been diagnosed with diarrhea-predominant Irritable bowel syndrome(IBS-D)
Group 0 sample size Number of subjects in the control (unexposed) group
Group 1 sample size Number of subjects in the case (exposed) group
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
2 Months prior to the study.

Lab analysis

Sequencing type
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Non-quantitative PCR

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)
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-28

Curated date: 2024/02/28

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: Table 2, Table 3.

Description: Percent contribution of predominant T-RFs in fecal and mucosal samples from healthy controls and D-IBS patients.

Values are means ± SE of normalized terminal-restriction fragment (T-RF) peak abundance from top 90% of contributors (predominant contributors) within each group. Predicted bacterial group refers to bacterial phylum, class, order, or family assigned to a T-RF based on the resolution of the Microbial Community Analysis (MiCA) database (41). NBG, numerous bacterial groups (i.e., MiCA database provided a large number of bacterial groups for this T-RF that are too numerous to list); NC, no contribution (i.e., T-RF does not contribute to the top 90% of T-RFs in a sample). Underlined bacterial groups are those consistently identified by T-RFs generated from 3 restriction enzymes (Hha I, Hae III, and Msp I) that contributed 90% of microbiota in healthy controls but not D-IBS patients. Significantly different from % contribution in healthy controls:

Table 3. Hae III- and Msp I-generated T-RFs that contribute to 90% of the fecal microbiota in healthy controls but not D-IBS patients

Abundance in Group 1: decreased abundance in IBS-D

NCBI Quality ControlLinks
Clostridiales bacterium

Revision editor(s): Peace Sandy