Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome

Study information

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study design

case-control

Citation

PMID PubMed identifier for scientific articles.

22339879

DOI Digital object identifier for electronic documents.

10.1111/j.1365-2982.2012.01891.x

URI

Authors

Carroll IM, Ringel-Kulka T, Siddle JP, Ringel Y

Journal

Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society

Year

2012

BACKGROUND: The intestinal microbiota has been implicated in the pathophysiology of irritable bowel syndrome (IBS). Due to the variable resolutions of techniques used to characterize the intestinal microbiota, and the heterogeneity of IBS, the defined alterations of the IBS intestinal microbiota are inconsistent. We analyzed the composition of the intestinal microbiota in a defined subgroup of IBS patients (diarrhea-predominant IBS, D-IBS) using a technique that provides the deepest characterization available for complex microbial communities. METHODS: Fecal DNA was isolated from 23 D-IBS patients and 23 healthy controls (HC). Variable regions V1-V3 and V6 of the 16S rRNA gene were amplified from all samples. PCR products were sequenced using 454 high throughput sequencing. The composition, diversity and richness of microbial communities were determined and compared between D-IBS and HC using the quantitative insights into microbial ecology pipeline. KEY RESULTS: The contribution of bacterial groups to the composition of the intestinal microbiota differed between D-IBS and HC. D-IBS patients had significantly higher levels of Enterobacteriaceae (P = 0.03), and lower levels of Fecalibacterium genera (P = 0.04) compared to HC. β-Diversity values demonstrated significantly lower levels of UniFrac distances in HC compared to D-IBS patients. The richness of 16S rRNA sequences was significantly decreased in D-IBS patients (P < 0.04). CONCLUSIONS & INFERENCES: Our 16S rRNA sequence data demonstrates a community-level dysbiosis in D-IBS. The altered composition of the intestinal microbiota in D-IBS is associated with significant increases in detrimental and decreases in beneficial bacterial groups, and a reduction in microbial richness.

Experiment 1

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Curated date: 2021/01/10

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Revision editor(s): WikiWorks, LGeistlinger, Rimsha, Victoria

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 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

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 controls

Group 1 name Corresponds to the case (exposed) group for case-control studies: diarrhea-predominant irritable bowel syndrome

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Diarrhea-Predominant irritable bowel syndrome

Group 0 sample size Number of subjects in the control (unexposed) group: 23

Group 1 sample size Number of subjects in the case (exposed) group: 23

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: 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).: raw counts

Statistical test: T-Test

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

Richness Number of species: decreased

Signature 1

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Source: Table 2

Description: Bacterial taxa that differ between D-IBS patients and healthy controls

Abundance in Group 1: increased abundance in diarrhea-predominant irritable bowel syndrome

NCBI	Quality Control	Links
Enterobacterales
Enterobacteriaceae

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Signature 2

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Curated date: 2021/01/10

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Revision editor(s): WikiWorks

Source: Table 2

Description: Bacterial taxa that differ between D-IBS patients and healthy controls

Abundance in Group 1: decreased abundance in diarrhea-predominant irritable bowel syndrome

NCBI	Quality Control	Links
Faecalibacterium

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Experiment 2

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Curated date: 2021/01/10

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Differences from previous experiment shown

Subjects

Lab analysis

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V6

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: Not specified