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

Study information

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

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

21737778

DOI Digital object identifier for electronic documents.

https://doi.org/10.1152%2Fajpgi.00154.2011

URI

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3220325/

Authors

Carroll IM, Ringel-Kulka T, Keku TO, Chang YH, Packey CD, Sartor RB, Ringel Y

Journal

American journal of physiology. Gastrointestinal and liver physiology

Year

2011

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

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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, KateRasheed

Subjects

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

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: IBS-D

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: 21

Group 1 sample size Number of subjects in the case (exposed) group: 16

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 2 months

Lab analysis

Sequencing type: PCR

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): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

Alpha Diversity

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

Signature 1

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

Curated date: 2024/02/28

Curator: Peace Sandy

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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 Control	Links
Clostridiales bacterium
Planctomycetaceae

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