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

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

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

Characterization of the nasal and oral microbiota of detection dogs

<div><p>Little is known about physiological factors that affect the sense of olfaction in dogs. The objectives of this study were to describe the canine nasal and oral microbiota in detection dogs. We sought to determine the bacterial composition of the nasal and oral microbiota of a diverse population of detection canines. Nasal and oral swabs were collected from healthy dogs (n = 81) from four locations—Alabama, Georgia, California, and Texas. Nasal and oral swabs were also collected from a second cohort of detection canines belonging to three different detection job categories: explosive detection dogs (SP-E; n = 22), patrol and narcotics detection dogs (P-NDD; n = 15), and vapor wake dogs (VWD-E; n = 9). To understand if the nasal and oral microbiota of detection canines were variable, sample collection was repeated after 7 weeks in a subset of dogs. DNA was extracted from the swabs and used for 454-pyrosequencing of the16S rRNA genes. Nasal samples had a significantly lower diversity than oral samples (<i>P</i><0.01). Actinobacteria and Proteobacteria were higher in nasal samples, while Bacteroidetes, Firmicutes, Fusobacteria, and Tenericutes were higher in oral samples. Bacterial diversity was not significantly different based on the detection job. No significant difference in beta diversity was observed in the nasal samples based on the detection job. In oral samples, however, ANOSIM suggested a significant difference in bacterial communities based on job category albeit with a small effect size (R = 0.1079, <i>P</i> = 0.02). Analysis of the composition of bacterial communities using LEfSe showed that within the nasal samples, <i>Cardiobacterium</i> and <i>Riemerella</i> were higher in VWD-E dogs, and <i>Sphingobacterium</i> was higher in the P-NDD group. In the oral samples <i>Enterococcus</i> and <i>Capnocytophaga</i> were higher in the P-NDD group. <i>Gemella</i> and <i>Aggregatibacter</i> were higher in S-PE, and <i>Pigmentiphaga</i>, <i>Chryseobacterium</i>, <i>Parabacteroides</i> amongst others were higher within the VWD-E group. Our initial data also shows that there is a temporal variation in alpha diversity in nasal samples in detection canines.</p></div

Bacterial diversity measures of samples based on job category of detection dogs in cohort 2 from nasal and oral samples.

<p>Lines represent the mean of each group, while the error bars represent the standard deviations. Beta diversity: Principal coordinate analysis (PCoA) of unweighted UniFrac distances of 16S rRNA genes. Analysis of similarity (ANOSIM) for B) nasal (R = 0.05; <i>P</i> = 0.19) and D) oral samples (R = 0.11, <i>P</i> = 0.02).</p

Linear discriminant analysis of bacterial genera and their associations with detection jobs.

<p>Only LDA scores of >3.0 are shown.</p

Summary of alpha diversity indices of samples from Labradors at a depth of 4,600 sequences per sample based on location.

<p>Summary of alpha diversity indices of samples from Labradors at a depth of 4,600 sequences per sample based on location.</p