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Comparative Study
, 7 (12), e51907

The Fecal Microbiome in Dogs With Acute Diarrhea and Idiopathic Inflammatory Bowel Disease

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Comparative Study

The Fecal Microbiome in Dogs With Acute Diarrhea and Idiopathic Inflammatory Bowel Disease

Jan S Suchodolski et al. PLoS One.

Abstract

Background: Recent molecular studies have revealed a highly complex bacterial assembly in the canine intestinal tract. There is mounting evidence that microbes play an important role in the pathogenesis of acute and chronic enteropathies of dogs, including idiopathic inflammatory bowel disease (IBD). The aim of this study was to characterize the bacterial microbiota in dogs with various gastrointestinal disorders.

Methodology/principal findings: Fecal samples from healthy dogs (n = 32), dogs with acute non-hemorrhagic diarrhea (NHD; n = 12), dogs with acute hemorrhagic diarrhea (AHD; n = 13), and dogs with active (n = 9) and therapeutically controlled idiopathic IBD (n = 10) were analyzed by 454-pyrosequencing of the 16S rRNA gene and qPCR assays. Dogs with acute diarrhea, especially those with AHD, had the most profound alterations in their microbiome, as significant separations were observed on PCoA plots of unweighted Unifrac distances. Dogs with AHD had significant decreases in Blautia, Ruminococcaceae including Faecalibacterium, and Turicibacter spp., and significant increases in genus Sutterella and Clostridium perfringens when compared to healthy dogs. No significant separation on PCoA plots was observed for the dogs with IBD. Faecalibacterium spp. and Fusobacteria were, however, decreased in the dogs with clinically active IBD, but increased during time periods of clinically insignificant IBD, as defined by a clinical IBD activity index (CIBDAI).

Conclusions: Results of this study revealed a bacterial dysbiosis in fecal samples of dogs with various GI disorders. The observed changes in the microbiome differed between acute and chronic disease states. The bacterial groups that were commonly decreased during diarrhea are considered to be important short-chain fatty acid producers and may be important for canine intestinal health. Future studies should correlate these observed phylogenetic differences with functional changes in the intestinal microbiome of dogs with defined disease phenotypes.

Conflict of interest statement

Competing Interests: The authors have read the journal’s policy and have the following conflict. Author Scot E. Dowd is an employee of MR DNA (Molecular Research), Shallowater. There are no patents, products in development or marketed products to declare. This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors.

Figures

Figure 1
Figure 1. Rarefaction analysis of 16 S rRNA gene sequences obtained from canine fecal samples.
Lines represent the average of each group, while the error bars represent the standard deviations. The analysis was performed on a randomly selected subset of 2,000 sequences per sample. A_IBD = active IBD; S_IBD = therapeutically controlled IBD; NHD = acute non-hemorrhagic diarrhea; AHD = acute hemorrhagic diarrhea.
Figure 2
Figure 2. Principal Coordinates Analysis (PCoA) of unweighted UniFrac distances of 16 S rRNA genes.
(A) Analysis for healthy dogs (blue), dogs with acute non-hemorrhagic diarrhea (NHD; green), and dogs with acute hemorrhagic diarrhea (AHD; red). These results indicate that fecal microbial communities differ in dogs with acute forms of diarrhea compared to healthy control dogs. Statistical analysis revealed a significant separation between samples obtained from NHD and AHD (ANOSIM; p = 0.004) and both groups were also significantly different from the healthy dogs (ANOSIM; NHD vs. healthy dogs, p = 0.003; AHD vs. healthy dogs, p = 0.001). (B) Analysis for healthy dogs (blue), dogs with active IBD (red), and dogs with therapeutically controlled IBD (green). In contrast to the dogs with acute diarrhea, fecal communities in dogs with chronic forms of diarrhea (active idiopathic IBD) were not significantly different from healthy dogs in this study.
Figure 3
Figure 3. Results of sequence analysis for selected bacterial groups.
H = healthy, NHD = acute non-hemorrhagic diarrhea, AHD = acute hemorrhagic diarrhea, A_IBD = active IBD, S_IBD = therapeutically controlled, clinically insignificant IBD. Columns not sharing a common superscript are significantly different (P<0.05).
Figure 4
Figure 4. Results of quantitative PCR assays for selected bacterial groups.
H = healthy, NHD = acute non-hemorrhagic diarrhea, AHD = acute hemorrhagic diarrhea, A_IBD = active IBD, S_IBD = therapeutically controlled, clinically insignificant IBD. Columns not sharing a common superscript are significantly different (P<0.05).
Figure 5
Figure 5. Faecalibacterium spp. and the phylum Fusobacteria in active and non-active IBD.
Using qPCR, paired fecal samples were analyzed from dogs (n = 8) at time periods of active and clinically insignificant IBD as scored by a clinical IBD disease activity index (CIBDAI). The time period between the collections of repeated samples ranged from 2–8 months (median 5.5 months). None of the other bacterial groups evaluated by qPCR, including total bacteria, revealed significant differences between the paired time periods.
Figure 6
Figure 6. Heatmap illustrating the relative abundance of predominant bacterial families in fecal samples of healthy dogs and dogs with acute diarrhea based on 454-pyrosequencing.
Samples from healthy dogs (H), dogs with acute non-hemorrhagic diarrhea (NHD), and dogs with acute hemorrhagic diarrhea (AHD) are shown. The heatmap represents the relative percentage of each family within each sample.

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