Table 1.
Relative abundances of bacterial phyla, families, and genera in cecal and fecal samples of female Ossabaw swine fed low-fat diet (lean) or Western diet (Obese) for 36 wk
| Lean (n = 4 each) |
Obese (n = 3 each) |
P Value |
|||||
|---|---|---|---|---|---|---|---|
| Cecal | Fecal | Cecal | Fecal | Sample Type | Body Composition | Interaction | |
| Unassigned* | 0.13 ± 0.05 | 0.23 ± 0.13 | 3.27 ± 1.47 | 2.10 ± 1.44 | 0.5512 | 0.0158 | 0.4808 |
| Methanobrevibacter | 0.05 ± 0.03 | 0.08 ± 0.03 | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.5250 | 0.0067 | 0.5250 |
| Methanosphaera | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.20 ± 0.10 | 1.80 ± 0.71 | 0.1087 | 0.0441 | 0.1087 |
| Actinobacteria | 0.18 ± 0.06 | 0.00 ± 0.00 | 0.13 ± 0.09 | 1.63 ± 0.61 | 0.0296 | 0.0123 | 0.0094 |
| Coriobacteriaceae† | 0.10 ± 0.04 | 0.00 ± 0.00 | 0.13 ± 0.09 | 1.60 ± 0.61 | 0.0245 | 0.0101 | 0.0126 |
| Unassigned | 0.10 ± 0.04 | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.20 ± 0.10 | 0.3250 | 0.3250 | 0.0111 |
| Collinsella‡ | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.13 ± 0.09 | 1.33 ± 0.54 | 0.0265 | 0.0096 | 0.0265 |
| Bacteroidetes | 45.1 ± 3.32 | 45.0 ± 1.59 | 34.8 ± 3.23 | 10.9 ± 1.85 | 0.0011 | <.0001 | 0.4348 |
| Unassigned | 15.7 ± 3.37 | 7.55 ± 1.94 | 0.10 ± 0.06 | 0.00 ± 0.00 | 0.1035 | 0.0005 | 0.1111 |
| Bacteroidaceae | 0.28 ± 0.05 | 0.15 ± 0.06 | 1.57 ± 1.03 | 0.37 ± 0.12 | 0.1588 | 0.1137 | 0.2449 |
| Porphyromonadaceae | 0.18 ± 0.09 | 1.18 ± 0.33 | 0.07 ± 0.03 | 0.10 ± 0.00 | 0.0277 | 0.0146 | 0.0368 |
| Parabacteroides | 0.18 ± 0.09 | 1.15 ± 0.33 | 0.07 ± 0.03 | 0.10 ± 0.00 | 0.0359 | 0.0193 | 0.0471 |
| Prevotellaceae | 9.18 ± 2.73 | 10.2 ± 0.60 | 26.6 ± 4.17 | 9.57 ± 1.72 | 0.0093 | 0.0072 | 0.0049 |
| RF16 | 0.08 ± 0.03 | 0.15 ± 0.06 | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.3814 | 0.0206 | 0.3814 |
| Rikenellaceae | 0.25 ± 0.22 | 0.30 ± 0.15 | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.8755 | 0.1076 | 0.8755 |
| S24-7 | 1.78 ± 0.38 | 2.95 ± 0.70 | 2.90 ± 1.96 | 0.70 ± 0.06 | 0.5999 | 0.5654 | 0.1048 |
| Paraprevotellaceae | 16.5 ± 1.56 | 12.2 ± 2.09 | 3.53 ± 1.19 | 0.17 ± 0.03 | 0.0404 | <.0001 | 0.7854 |
| Unassigned | 0.93 ± 0.50 | 0.43 ± 0.20 | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.4492 | 0.0594 | 0.4492 |
| CF231 | 4.53 ± 1.41 | 1.48 ± 0.19 | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.1001 | 0.0051 | 0.1001 |
| YRC22 | 5.85 ± 0.94 | 5.90 ± 0.66 | 0.03 ± 0.03 | 0.00 ± 0.00 | 0.9952 | <.0001 | 0.9666 |
| Prevotella | 5.13 ± 1.29 | 4.38 ± 1.97 | 3.47 ± 1.19 | 0.17 ± 0.03 | 0.2012 | 0.0727 | 0.4187 |
| p-2534-18B | 0.95 ± 0.49 | 10.3 ± 2.92 | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.0238 | 0.0094 | 0.0238 |
| Cyanobacteria | 0.03 ± 0.03 | 0.00 ± 0.00 | 1.03 ± 0.55 | 0.33 ± 0.12 | 0.1547 | 0.0173 | 0.1823 |
| Firmicutes | 39.5 ± 3.46 | 40.9 ± 1.37 | 34.5 ± 8.75 | 48.0 ± 1.94 | 0.1188 | 0.8192 | 0.1947 |
| Lactobacillaceae | 5.10 ± 2.57 | 0.05 ± 0.03 | 8.23 ± 3.83 | 6.47 ± 2.67 | 0.1987 | 0.0826 | 0.5223 |
| Streptococcaceae | 2.10 ± 1.35 | 0.13 ± 0.03 | 1.90 ± 1.14 | 5.97 ± 2.88 | 0.5077 | 0.0936 | 0.0753 |
| Turicibacteraceae | 0.53 ± 0.17 | 0.48 ± 0.09 | 0.00 ± 0.00 | 0.03 ± 0.03 | 0.9429 | 0.0017 | 0.7212 |
| Clostridiales (other) | 0.43 ± 0.13 | 0.48 ± 0.10 | 0.17 ± 0.07 | 0.13 ± 0.03 | 0.9375 | 0.0160 | 0.6961 |
| Unassigned | 6.75 ± 0.89 | 6.65 ± 0.68 | 0.93 ± 0.83 | 0.93 ± 0.39 | 0.9124 | <.0001 | 0.9124 |
| Christensenellaceae | 0.10 ± 0.07 | 0.43 ± 0.10 | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.0527 | 0.0053 | 0.0527 |
| Clostridiaceae | 1.33 ± 0.41 | 2.58 ± 0.37 | 0.17 ± 0.12 | 0.63 ± 0.22 | 0.0319 | 0.0011 | 0.2820 |
| Unassigned | 0.53 ± 0.26 | 2.00 ± 0.46 | 0.10 ± 0.10 | 0.53 ± 0.24 | 0.0130 | 0.0094 | 0.1593 |
| Clostridium | 0.75 ± 0.21 | 0.55 ± 0.15 | 0.07 ± 0.03 | 0.07 ± 0.07 | 0.5308 | 0.0036 | 0.5308 |
| Lachnospiraceae | 11.1 ± 2.49 | 9.05 ± 1.45 | 3.83 ± 1.30 | 9.00 ± 0.67 | 0.4030 | 0.0729 | 0.0763 |
| Other | 0.68 ± 0.17 | 0.25 ± 0.09 | 0.03 ± 0.03 | 0.20 ± 0.06 | 0.2829 | 0.0125 | 0.0265 |
| Unassigned | 3.65 ± 0.84 | 5.20 ± 0.89 | 1.87 ± 0.43 | 4.47 ± 0.52 | 0.0236 | 0.1368 | 0.5150 |
| Blautia | 0.18 ± 0.09 | 0.00 ± 0.00 | 0.40 ± 0.12 | 1.43 ± 0.47 | 0.0653 | 0.0025 | 0.0155 |
| Coprococcus | 0.65 ± 0.13 | 0.28 ± 0.06 | 0.40 ± 0.26 | 1.47 ± 0.88 | 0.4025 | 0.2614 | 0.0984 |
| Dorea | 5.20 ± 2.37 | 2.83 ± 0.87 | 0.70 ± 0.50 | 0.60 ± 0.12 | 0.4316 | 0.0501 | 0.4687 |
| Lachnospira | 0.35 ± 0.09 | 0.18 ± 0.05 | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.2664 | 0.0022 | 0.1141 |
| Roseburia | 0.25 ± 0.12 | 0.13 ± 0.09 | 0.03 ± 0.03 | 0.03 ± 0.03 | 0.5128 | 0.1251 | 0.5128 |
| Ruminococcus | 0.10 ± 0.00 | 0.23 ± 0.10 | 0.40 ± 0.20 | 0.67 ± 0.23 | 0.0005 | <.0001 | 0.0001 |
| Peptostreptococcaceae | 0.10 ± 0.04 | 0.00 ± 0.00 | 0.10 ± 0.10 | 1.50 ± 0.80 | 0.0842 | 0.0513 | 0.0513 |
| Ruminococcaceae | 9.85 ± 1.46 | 19.4 ± 1.39 | 1.30 ± 0.55 | 4.80 ± 2.07 | 0.0014 | <.0001 | 0.0691 |
| Other | 0.03 ± 0.03 | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.4178 | 0.4178 | 0.4178 |
| Unassigned | 7.08 ± 1.44 | 18.2 ± 1.45 | 1.10 ± 0.45 | 4.37 ± 1.94 | 0.0006 | <.0001 | 0.0238 |
| Ruminococcus | 1.65 ± 0.18 | 0.35 ± 0.03 | 0.03 ± 0.03 | 0.13 ± 0.09 | 0.0005 | <.0001 | 0.0001 |
| Veillonellaceae | 1.40 ± 0.40 | 0.53 ± 0.05 | 17.6 ± 1.39 | 17.2 ± 3.61 | 0.7121 | <.0001 | 0.8796 |
| Unassigned | 0.08 ± 0.05 | 0.03 ± 0.03 | 1.00 ± 0.30 | 0.93 ± 0.58 | 0.8372 | 0.0078 | 0.9766 |
| Acidaminococcus | 0.00 ± 0.00 | 0.00 ± 0.00 | 1.10 ± 0.75 | 0.43 ± 0.12 | 0.3192 | 0.0366 | 0.3192 |
| Anaerovibrio | 0.43 ± 0.20 | 0.00 ± 0.00 | 1.80 ± 0.57 | 0.23 ± 0.07 | 0.0040 | 0.0132 | 0.0587 |
| Megamonas | 0.00 ± 0.00 | 0.00 ± 0.00 | 3.50 ± 1.85 | 5.23 ± 3.43 | 0.6070 | 0.0233 | 0.6070 |
| Megasphaera | 0.03 ± 0.03 | 0.00 ± 0.00 | 4.93 ± 1.87 | 6.73 ± 0.71 | 0.3130 | <.0001 | 0.3003 |
| Mitsuokella | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.07 ± 0.03 | 0.13 ± 0.03 | 0.1218 | 0.0005 | 0.1218 |
| Phascolarctobacterium | 0.70 ± 0.19 | 0.45 ± 0.06 | 5.20 ± 1.79 | 3.57 ± 0.85 | 0.2866 | 0.0011 | 0.4277 |
| Veillonella | 0.13 ± 0.08 | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.1893 | 0.1893 | 0.1893 |
| Eubacterium | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.06 ± 0.06 | 0.16 ± 0.03 | 0.1399 | 0.0038 | 0.1399 |
| p-75-a5 | 0.68 ± 0.17 | 0.93 ± 0.34 | 0.00 ± 0.00 | 0.06 ± 0.03 | 0.5008 | 0.0070 | 0.6944 |
| Fusobacteria | 0.00 ± 0.00 | 0.00 ± 0.00 | 9.73 ± 2.29 | 10.1 ± 3.83 | 0.9167 | 0.0003 | 0.9167 |
| Proteobacteria | 0.43 ± 0.17 | 0.00 ± 0.00 | 16.1 ± 3.55 | 25.1 ± 7.45 | 0.2428 | 0.0002 | 0.2024 |
| Desulfovibrionaceae | 0.03 ± 0.03 | 0.00 ± 0.00 | 1.73 ± 0.34 | 0.60 ± 0.26 | 0.0093 | <.0001 | 0.0118 |
| Unassigned | 0.03 ± 0.03 | 0.00 ± 0.00 | 1.30 ± 0.20 | 0.07 ± 0.03 | <.0001 | <.0001 | <.0001 |
| Bilophila | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.06 ± 0.03 | 0.10 ± 0.06 | 0.5634 | 0.0136 | 0.5634 |
| Desulfovibrio | 0.03 ± 0.03 | 0.00 ± 0.00 | 0.33 ± 0.15 | 0.43 ± 0.20 | 0.7294 | 0.0056 | 0.5663 |
| Campylobacteraceae | 0.25 ± 0.12 | 0.00 ± 0.00 | 0.20 ± 0.20 | 0.00 ± 0.00 | 0.1063 | 0.1063 | 0.1063 |
| Succinivibrionaceae | 0.00 ± 0.00 | 0.00 ± 0.00 | 13.3 ± 4.16 | 15.2 ± 6.21 | 0.7715 | 0.0010 | 0.7715 |
| Succinivibrio | 0.00 ± 0.00 | 0.00 ± 0.00 | 13.3 ± 4.12 | 15.2 ± 6.21 | 0.7670 | 0.0010 | 0.7670 |
| Enterobacteriaceae | 0.03 ± 0.03 | 0.00 ± 0.00 | 1.03 ± 0.46 | 9.27 ± 5.74 | 0.1191 | 0.0587 | 0.1172 |
| Spirochaetes | 7.28 ± 2.05 | 3.15 ± 0.92 | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.1519 | 0.0029 | 0.1519 |
| Tenericutes | 6.70 ± 1.65 | 9.70 ± 2.18 | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.3749 | 0.0005 | 0.3749 |
| Verrucomicrobia | 0.60 ± 0.32 | 0.83 ± 0.27 | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.6567 | 0.0158 | 0.6567 |
| RFP12 | 0.25 ± 0.12 | 0.73 ± 0.23 | 0.00 ± 0.00 | 0.00 ± 0.00 | 0.1284 | 0.0078 | 0.1284 |
All values are means ± SE. Boldface P value denotes a significant difference. Relative abundances of
*
bacterial phyla,
†
families,
‡
and genera.