The fecal microbiome in dogs with acute diarrhea and idiopathic inflammatory bowel disease.

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. 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). 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

<i>Faecalibacterium</i> spp. and the phylum Fusobacteria in active and non-active IBD.

<p>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.</p

Oligonucleotides primers/probes used in this study.

<p>Oligonucleotides primers/probes used in this study.</p

Results of quantitative PCR assays for selected bacterial groups.

<p>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).</p

Summary statistics for qPCR results.

*<p>Medians not sharing a common superscript are significantly different (p<0.05 based on a Dunn’s multiple comparisons test).</p><p>NHD = acute non-hemorrhagic diarrhea; AHD = acute hemorrhagic diarrhea; IBD = inflammatory bowel disease</p

Relative percentages of the most abundant bacterial groups at the various phylogenetic levels (phylum, class, order, family, genus) based on pyrosequencing.

<p>Taxa present in at least 50% of dogs (either healthy or diseased) included in analysis.</p>**<p>p-values adjusted based on the Benjamini and Hochberg False discovery rate.</p>*<p>Medians not sharing a common superscript are significantly different (p<0.05 based on a Dunn’s multiple comparisons test).</p><p>NHD = acute hemorrhagic diarrhea; AHD = acute hemorrhagic diarrhea; IBD = inflammatory bowel disease.</p

Results of sequence analysis for selected bacterial groups.

<p>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).</p

Rarefaction analysis of 16 S rRNA gene sequences obtained from canine fecal samples.

<p>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.</p

Heatmap illustrating the relative abundance of predominant bacterial families in fecal samples of healthy dogs and dogs with acute diarrhea based on 454-pyrosequencing.

<p>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.</p

Summary of basic characteristics and alpha diversity measures.

<p>IBD = inflammatory bowel disease.</p><p>CIBDAI = canine IBD disease activity index.</p><p>NHD = acute non-hemorrhagic diarrhea, AHD = acute hemorrhagic diarrhea, A_IBD = active IBD, S_IBD = clinically insignificant IBD.</p