Table 3.
Relative proportions of predominant bacterial taxa in the duodenal samples.
| Relative Abundance % (Min–Max) of Sequences | |||
|---|---|---|---|
| Phylum/Class/Order/Family/Genus | HC (n = 7) | IBD (n = 30) | p-Value |
| Actinobacteria | 4.86 (0.24–13.85) | 8.23 (0.00–19.16) | 0.362 |
| Actinobacteria | 4.60 (0.23–13.85) | 3.84 (0.00–17.87) | 0.362 |
| Actinomycetales | 0.57 (0.00–3.19) | 0.46 (0.00–5.90) | 0.518 |
| Actinomycetaceae | 0.57 (0.00–3.19) | 0.46 (0.00–5.90) | 0.518 |
| Actinomyces | 0.57 (0.00–3.19) | 0.46 (0.00–5.90) | 0.518 |
| Bifidobacteriales | 2.78 (0.00–13.85) | 2.28 (0.00–12.10) | 1.000 |
| Bifidobacteriaceae | 2.78 (0.00–13.85) | 2.28 (0.00–12.10) | 1.000 |
| Bifidobacterium | 2.78 (0.00–13.85) | 2.28 (0.00–12.1) | 1.000 |
| Corynebacteriales | 1.09 (0.00–6.48) | 0.42 (0.00–3.06) | 0.746 |
| Rubrobacteria | 0.18 (0.00–1.06) | 0.03 (0.00–0.64) | 0.002 * |
| Rubrobacterales | 0.18 (0.00–1.06) | 0.03 (0.00–0.64) | 0.002 * |
| Rubrobacteriaceae | 0.18 (0.00–1.06) | 0.03 (0.00–0.64) | 0.002 * |
| Rubrobacter | 0.18 (0.00–1.06) | 0.03 (0.00–0.64) | 0.002 * |
| Bacteroidetes | 6.83 (0.00–20.52) | 6.81 (0.00–34.39) | 0.954 |
| Bacteroidia | 6.74 (0.00–20.52) | 6.80 (0.00–34.39) | 1.000 |
| Bacteroidales | 1.05 (0.00–3.72) | 2.85 (0.00–34.16) | 0.331 |
| Flavobacteriales | 5.67 (0.00–20.52) | 3.79 (0.00–33.84) | 0.493 |
| Weeksellaceae | 5.46 (0.00–19.83) | 3.66 (0.00–3.67) | 0.419 |
| Chryseobacterium | 2.30 (0.00–11.29) | 3.44 (0.00–33.67) | 0.884 |
| Cyanobacteria | 1.86 (0.00–6.48) | 0.44 (0.00–5.73) | 0.010 * |
| Vampirivibrionia | 0.58 (0.00–1.82) | 0.04 (0.00–0.83) | 0.005 * |
| Obscuribacterales | 0.58 (0.00–1.82) | 0.04 (0.00–0.83) | 0.005 * |
| Obscuribacteraceae | 0.58 (0.00–1.82) | 0.04 (0.00–0.83) | 0.005 * |
| Firmicutes | 26.89 (0.38–60.64) | 39.82 (1.02–99.71) | 0.323 |
| Bacilli | 16.57 (0.11–60.19) | 21.06 (0.08–57.44) | 0.362 |
| Bacillales | 4.47 (0.00–14.81) | 5.75 (0.00–27.36) | 0.786 |
| Bacillaceae | 4.47 (0.00–14.81) | 5.75 (0.00–27.36) | 0.786 |
| Anaerobacillus | 2.82 (0.00–10.41) | 2.41 (0.00–5.90) | 0.953 |
| Bacillus | 1.65 (0.00–6.48) | 3.28 (0.00.18.24) | 0.389 |
| Lactobacillales | 8.39 (0.03–30.13) | 11.97 (0.00–40.64) | 0.522 |
| Lactobacillaceae | 4.85 (0.00–30.13) | 3.15 (0.00–24.66) | 0.905 |
| Lactobacillus | 4.85 (0.00–30.13) | 3.15 (0.00–24.66) | 0.905 |
| Streptococcaceae | 2.14 (0.00–7.14) | 6.73 (0.00–23.12) | 0.340 |
| Streptococcus | 2.14 (0.00–7.14) | 6.73 (0.00–23.12) | 0.340 |
| Staphylococcales | 3.64 (0.00–15.26) | 0.785 (0.00–4.29) | 0.202 |
| Gemellaceae | 0.54 (0.00–2.38) | 0.28 (0.00–2.52) | 0.275 |
| Gemella | 0.54 (0.00–2.38) | 0.28 (0.00–2.52) | 0.275 |
| Staphylococcaceae | 3.11 (0.00–15.26) | 0.50 (0.00–4.29) | 0.134 |
| Staphylococcus | 3.10 (0.00–15.26) | 0.50 (0.00–4.29) | 0.256 |
| Clostridia | 9.87 (0.10–26.19) | 18.64 (0.00–99.63) | 0.627 |
| Clostridiales | 3.35 (0.00–21.03) | 3.49 (0.00–56.33) | 0.767 |
| Clostridiaceae | 3.35 (0.00–21.03) | 3.49 (0.00–56.33) | 0.767 |
| Clostridium sensu stricto 1 | 0.39 (0.00–1.50) | 3.33 (0.00–52.55) | 0.899 |
| Lachnospirales | 1.42 (0.00–4.63) | 9.28 (0.00–32.81) | 0.284 |
| Lachnospiraceae | 1.37 (0.00–4.63) | 9.24 (0.00–32.81) | 0.319 |
| Peptostreptococcales–Tissierellales | 3.67 (0.00–14.02) | 5.53 (0.00–92.26) | 0.876 |
| Peptostreptococcaceae | 2.95 (0.00–14.02) | 5.44 (0.00–92.26) | 0.740 |
| Romboutsia | 2.25 (0.00–14.02) | 3.37 (0.00–92.26) | 0.407 |
| Proteobacteria | 57.14 (15.83–77.81) | 40.54 (0.27–6.65) | 0.222 |
| Alphaproteobacteria | 7.61 (0.58–23.33) | 6.46 (0.00–30.02) | 0.574 |
| Caulobacterales | 1.92 (0.00–9.93) | 0.59 (0.00–3.80) | 0.441 |
| Caulobacteraceae | 1.92 (0.00–9.93) | 0.59 (0.00–3.80) | 0.441 |
| Phenylobacterium | 1.92 (0.00–9.93) | 0.59 (0.00–3.73) | 0.441 |
| Rhizobiales | 2.45 (0.07–8.12) | 2.22 (0.00–11.47) | 0.402 |
| Beijerinckiaceae | 1.03 (0.00–5.00) | 0.72 (0.00–5.54) | 0.885 |
| Methylobacterium–Methylorubrum | 0.72 (0.00–4.78) | 0.57 (0.00–5.54) | 0.327 |
| Rhizobiaceae | 0.76 (0.00–2.56) | 0.92 (0.00–6.56) | 0.885 |
| Xanthobacteraceae | 0.60 (0.00–1.14) | 0.54 (0.00–4.66) | 0.163 |
| Bradyrhizobium | 0.41 (0.00–1.02) | 0.25 (0.00–3.99) | 0.059 |
| Sphingomonadales | 2.20 (0.37–6.35) | 3.22 (0.00–17.17) | 0.472 |
| Sphingomonadaceae | 2.20 (0.37–6.35) | 3.22 (0.00–5.29) | 0.472 |
| Sphingomonas | 2.00 (0.00–6.35) | 1.37 (0.00–14.44) | 0.132 |
| Gammaproteobacteria | 49.53 (13.41–73.79) | 34.08 (0.27–86.29) | 0.135 |
| Burkholderiales | 6.00 (1.46–12.16) | 4.25 (0.00–18.54) | 0.180 |
| Alcaligenaceae | 0.62 (0.00–1.90) | 0.85 (0.00–4.73) | 0.950 |
| Burkholderiaceae | 0.79 (0.00–2.48) | 0.98 (0.00–10.67) | 0.639 |
| Comamonadaceae | 1.99 (0.00–9.76) | 1.01 (0.00–4.08) | 0.352 |
| Delftia | 1.05 (0.00–5.30) | 0.74 (0.00–4.08) | 0.485 |
| Neisseriaceae | 1.68 (0.03–8.20) | 0.63 (0.00–5.32) | 0.004 * |
| Conchiformibius | 1.30 (0.00–5.80) | 0.41 (0.00–5.10) | 0.003 * |
| Enterobacterales | 2.78 (0.00–18.12) | 3.35 (0.00–15.84) | 0.534 |
| Enterobacteriaceae | 2.78 (0.00–18.12) | 3.30 (0.00–15.84) | 0.534 |
| Escherichia–Shigella | 1.92 (0.00–12.43) | 2.68 (0.00–15.84) | 0.471 |
| Pasteurellales | 3.26 (0.00–21.77) | 1.65 (0.00–18.07) | 0.383 |
| Pasteurellaceae | 3.26 (0.00–21.77) | 1.65 (0.00–18.07) | 0.383 |
| Pseudomonadales | 28.70 (3.17–56.64) | 14.33 (0.00–51.53) | 0.071 |
| Pseudomonadaceae | 26.38 (0.00–56.64) | 12.85 (0.00–51.53) | 0.174 |
| Pseudomonas | 26.38 (0.00–56.64) | 12.85 (0.00–51.53) | 0.167 |
| Xanthomonadales | 8.49 (0.00–24.44) | 10.16 (0.00–37.02) | 1.000 |
| Xanthomonadaceae | 8.49 (0.00–24.44) | 10.16 (0.00–37.02) | 1.000 |
| Stenotrophomonas | 8.36 (0.00–24.44) | 9.94 (0.00–36.91) | 0.968 |
IBD, inflammatory bowel disease; taxa present in at least 50% of the dogs (in any group) were included in this table. * p value < 0.05 using the Wilcoxon signed-rank test.