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

I M Carroll, T Ringel-Kulka, J P Siddle, Y Ringel, I M Carroll, T Ringel-Kulka, J P Siddle, Y Ringel

Abstract

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.

© 2012 Blackwell Publishing Ltd.

Figures

Figure 1
Figure 1
Percent contribution of bacterial genera, identified by 454 pyro-sequencing of the V1-3 16S rRNA gene region, to the fecal microbiota in (A) healthy controls, and (B) D-IBS patients. (C) Average abundance of the Faecalibacterium genus in fecal samples from D-IBS patients and healthy controls, based on V1-3 454 pyro-sequencing data. (D) Concentrations of Faecalibacterium prausnitzii in the fecal microbiota of D-IBS patients and healthy controls using qPCR. Statistical comparisons were carried out on the square root means of each group.
Figure 2
Figure 2
Variation in bacterial community composition between D-IBS patients and healthy controls. A significant decrease in average UniFrac distances was found in healthy controls when compared to the D-IBS group using weighted (A) and un-weighted (B) values for the V6 16S rRNA. All analyses represent the relationship between the microbiota in D-IBS and healthy control in fecal samples based on their β-diversity. Statistical comparisons were carried out on the square root means of each group.
Figure 3
Figure 3
Operational Taxonomic Unit (OTU) network analysis of bacterial communities from D-IBS patient and healthy control fecal samples for the V1-3 16S rRNA region. Nodes represent individual D-IBS samples (red circles), individual healthy control samples (green circles), and OTUs (white circles). Edges (lines) connecting D-IBS nodes (red edges) or healthy control nodes (green edges) to OTUs indicate whether a given OTU was found in that sample. The pattern of green and red edges indicates that although both groups share common OTUs, D-IBS samples share more OTUs in common and segregate from healthy control shared OTUs.
Figure 4
Figure 4
Rarefaction curves of D-IBS (broken line) patient and healthy control (solid line) fecal samples. Curves are based on α-diversity within sample groups for the V1-3 16S rRNA region. *Indicates significant differences between groups (p < 0.04). Statistical comparisons were carried out on the square root means of each group.

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