Average percentage of phyla identified in control dogs and dogs with IBD.

<p>Data represent the percentage of obtained total 16 S rRNA gene sequences. Error bars represent standard deviations.</p

Principal Coordinates Analysis (PCoA) of unweighted UniFrac distances of 16 S rRNA genes.

<p>The clustering indicates differences in microbiota composition between controls and dogs with IBD. The analysis was performed on a randomly selected subset of 840 sequences per sample. Because the samples clustered along Principal Coordinates (PC) 1 and PC 2, only these graphs are shown. <b>A – Analysis according to clinical severity of disease based on the Canine Inflammatory Bowel Disease Activity Index (CIBDAI)</b>. Control dogs (red) separated from dogs with idiopathic inflammatory bowel disease (IBD; blue = moderate CIBDAI; orange = severe CIBDAI) indicating differences in microbiota ecology. No clustering is observed according to the severity of clinical disease. <b>B – Analysis according to severity of histopathology</b>. Control dogs with normal histology (green) separated from dogs with idiopathic inflammatory bowel disease (IBD; blue = mild changes on histology; orange = moderate-to-severe changes on histology). A trend was observed for separation between dogs with mild and dogs with moderate-to-severe histological changes (ANOSIM, p = 0.07).</p

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

<p>Lines represent the average of each group (blue = control dogs; red = dogs with idiopathic inflammatory bowel disease), while the error bars represent the standard deviations. The analysis was performed on a randomly selected subset of 840 sequences per sample.</p

Principal Coordinates Analysis (PCoA) of unweighted UniFrac distances of 16 S rRNA.

<p>The analysis was performed on a randomly selected subset of 840 sequences per sample. The PCoA plots suggest that clustering was primarily based on intestinal disease rather than environmental factors. <b>A – Analysis according to clinical disease.</b> Control dogs (blue) cluster separately from dogs with IBD (red). <b>B – Age</b>. Blue symbols: dogs 3–4 years of age; orange: 5–6 years; green: 7–8 years; red: 12 years.<b>C – Gender.</b> Red = female dogs; Blue = male dogs. <b>D – Weeks between last dose of antibiotic administration and sample collection.</b> Green = 6 weeks; orange = 3 weeks; blue = 2 weeks; red = n/a (control dogs). <b>E – Fat content in diet.</b> Red = 2.5–4.0 grams of fat/100 kcal ME; blue = 4.1–5.0 grams of fat/100 kcal ME. <b>F – Protein content in diet.</b> Red = 4.0–5.9 grams of protein/100 kcal ME; blue 6.0–6.9 grams of protein/100 kcal ME; orange = 7.0–7.5 grams of protein/100 kcal ME.</p

Relative proportions of predominant bacterial taxa identified.

a<p>Mann-Whitney Test;</p>b<p>Fisher's exact test.</p>*<p><i>p</i>-values were adjusted for multiple comparisons based on the Benjamini and Hochberg False discovery rate.</p

Baseline characteristics of study dogs.

<p>CIBDAI = canine inflammatory bowel disease activity index.</p><p>IBD = inflammatory bowel disease.</p