Table 2. Genera identified in the caeca and crops with a MRA (%) > 1 in at least one treatment (i.e., day 1, high dose (HD) 14 and 35 days, low dose (LD) 14 and 35 days, control (C) 14 and 35 days).
| Mean relative abundance (%) (standard error) | |||||||
|---|---|---|---|---|---|---|---|
| Day 1 | HD 14d | HD 35d | LD 14d | LD 35d | C 14d | C35 d | |
| Caeca | |||||||
| Faecalibacterium | 3.272 (0.917) | 1.8 (0.088) | 9.827 (1.251) | 1.762 (0.066) | 9.08 (1.756) | 2.159 (0.136) | 5.617 (0.714) |
| Ruminococcus | 5.904 (0.86) | 8.995 (0.487) | 7.237 (0.2) | 10.173 (0.991) | 7.807 (0.336) | 9.072 (0.999) | 8.092 (0.537) |
| Eubacterium | 4.541 (0.834) | 7.153 (0.196) | 6.629 (0.08) | 7.309 (0.27) | 6.67 (0.101) | 7.071 (0.349) | 6.489 (0.256) |
| Bacteroides | 3.795 (0.528) | 7.824 (0.792) | 5.911 (0.211) | 6.806 (0.877) | 5.445 (0.303) | 7.427 (0.865) | 5.539 (0.419) |
| Clostridium | 15.108 (2.482) | 30.129 (1.687) | 26.298 (0.711) | 29.813 (0.829) | 25.812 (0.845) | 28.04 (1.594) | 23.775 (0.676) |
| Subdoligranulum | 2.461 (0.694) | 1.723 (0.144) | 2.963 (0.206) | 1.513 (0.076) | 3.947 (0.474) | 5.176 (2.221) | 4.588 (1.16) |
| Blautia | 1.881 (0.366) | 4.264 (0.587) | 2.388 (0.181) | 3.634 (0.354) | 2.403 (0.078) | 3.431 (0.463) | 3.217 (0.338) |
| Lactobacillus | 17.268 (4.092) | 1.956 (0.49) | 1.813 (0.351) | 1.93 (0.71) | 2.49 (0.439) | 1.155 (0.165) | 6.129 (1.509) |
| Bacillus | 1.169 (0.251) | 1.379 (0.088) | 1.612 (0.079) | 1.511 (0.165) | 1.476 (0.065) | 1.341 (0.055) | 1.462 (0.061) |
| Roseburia | 0.948 (0.154) | 1.621 (0.097) | 1.589 (0.042) | 1.619 (0.061) | 1.517 (0.063) | 1.519 (0.112) | 1.311 (0.062) |
| Butyrivibrio | 0.859 (0.172) | 1.56 (0.067) | 1.53 (0.036) | 1.631 (0.091) | 1.563 (0.05) | 1.634 (0.083) | 1.37 (0.043) |
| Ethanoligenens | 0.678 (0.116) | 1.235 (0.062) | 1.485 (0.021) | 1.422 (0.169) | 1.578 (0.049) | 1.766 (0.171) | 1.362 (0.14) |
| Holdemania | 0.753 (0.116) | 1.305 (0.048) | 1.433 (0.058) | 1.355 (0.063) | 1.379 (0.052) | 1.392 (0.035) | 1.23 (0.029) |
| Streptococcus | 1.019 (0.16) | 2.045 (0.553) | 1.41 (0.085) | 1.226 (0.07) | 1.357 (0.123) | 1.191 (0.086) | 1.224 (0.1) |
| Anaerotruncus | 0.655 (0.06) | 1.471 (0.102) | 1.26 (0.093) | 1.777 (0.226) | 1.386 (0.159) | 1.498 (0.135) | 1.094 (0.089) |
| Desulfitobacterium | 0.54 (0.135) | 1.043 (0.045) | 1.052 (0.029) | 1.092 (0.06) | 1.004 (0.03) | 1.111 (0.055) | 0.955 (0.031) |
| Dorea | 0.894 (0.138) | 1.37 (0.058) | 1.022 (0.028) | 1.384 (0.136) | 1.051 (0.043) | 1.251 (0.154) | 1.147 (0.08) |
| Coprococcus | 0.694 (0.097) | 1.077 (0.042) | 0.9 (0.012) | 1.108 (0.089) | 0.899 (0.033) | 0.992 (0.104) | 0.945 (0.056) |
| Enterococcus | 1.253 (0.268) | 0.843 (0.039) | 0.834 (0.02) | 0.827 (0.047) | 0.803 (0.015) | 0.712 (0.046) | 0.788 (0.048) |
| Escherichia | 7.608 (3.938) | 1.296 (0.433) | 0.497 (0.191) | 0.942 (0.386) | 0.686 (0.456) | 0.619 (0.225) | 1.008 (0.467) |
| Eggerthella | 0.436 (0.107) | 0.391 (0.015) | 0.45 (0.013) | 0.516 (0.026) | 0.468 (0.019) | 0.523 (0.043) | 1.072 (0.161) |
| Shigella | 1.148 (0.589) | 0.203 (0.072) | 0.075 (0.03) | 0.153 (0.065) | 0.105 (0.07) | 0.098 (0.036) | 0.157 (0.074) |
| Crops | |||||||
| Faecalibacterium | 1.248 (0.417) | 0.487 (0.191) | 0.158 (0.066) | 0.887 (0.153) | 0.092 (0.067) | 0.126 (0.015) | 0.056 (0.015) |
| Ruminococcus | 4.094 (1.287) | 2.559 (1.298) | 0.334 (0.155) | 2.535 (0.366) | 0.146 (0.1) | 0.495 (0.067) | 0.137 (0.048) |
| Eubacterium | 2.407 (0.724) | 1.389 (0.673) | 0.231 (0.095) | 1.475 (0.164) | 0.126 (0.076) | 0.374 (0.031) | 0.127 (0.029) |
| Bacteroides | 2.294 (0.455) | 0.799 (0.427) | 0.181 (0.078) | 1.149 (0.187) | 0.121 (0.08) | 0.262 (0.028) | 0.092 (0.02) |
| Clostridium | 9.578 (2.476) | 4.683 (2.122) | 0.918 (0.338) | 5.655 (0.506) | 0.485 (0.311) | 1.415 (0.098) | 0.483 (0.105) |
| Subdoligranulum | 1.597 (0.393) | 0.302 (0.095) | 0.125 (0.063) | 0.539 (0.066) | 0.085 (0.076) | 0.104 (0.014) | 0.051 (0.024) |
| Blautia | 1.579 (0.533) | 1.15 (0.57) | 0.152 (0.082) | 0.864 (0.116) | 0.053 (0.043) | 0.253 (0.022) | 0.049 (0.024) |
| Lactobacillus | 23.077 (5.819) | 59.931 (12.434) | 80.761 (6.911) | 55.188 (9.781) | 81.496 (14.061) | 79.209 (5.72) | 87.45 (4.139) |
| Bacillus | 0.993 (0.129) | 0.611 (0.158) | 0.576 (0.235) | 0.752 (0.212) | 0.171 (0.028) | 0.551 (0.13) | 0.332 (0.08) |
| Streptococcus | 0.699 (0.095) | 7.536 (4.791) | 1.134 (0.562) | 1.987 (0.272) | 0.612 (0.236) | 4.404 (2.505) | 1.708 (0.78) |
| Enterococcus | 0.628 (0.045) | 1.138 (0.446) | 0.982 (0.425) | 0.641 (0.072) | 0.385 (0.103) | 1.298 (0.279) | 1.05 (0.323) |
| Escherichia | 12.382 (6.287) | 0.878 (0.404) | 0.636 (0.287) | 3.344 (1.948) | 9.436 (9.311) | 2.092 (1.34) | 0.97 (0.801) |
| Staphylococcus | 0.27 (0.113) | 0.134 (0.023) | 3.001 (1.338) | 0.175 (0.038) | 0.276 (0.079) | 0.175 (0.035) | 1.014 (0.391) |
| Corynebacterium | 0.165 (0.117) | 0.031 (0.017) | 3.648 (2.112) | 0.046 (0.024) | 0.207 (0.058) | 0.011 (0.003) | 1.13 (0.79) |
| Shigella | 1.858 (0.988) | 0.11 (0.054) | 0.095 (0.043) | 0.491 (0.292) | 1.468 (1.446) | 0.312 (0.195) | 0.15 (0.123) |
| Xanthomonas | 1.859 (0.416) | 0.87 (0.595) | 0.039 (0.023) | 2.025 (1.183) | 0.043 (0.033) | 0.306 (0.047) | 0.012 (0.005) |
| Klebsiella | 0.137 (0.058) | 0.051 (0.024) | 0.033 (0.012) | 1.016 (0.627) | 0.188 (0.171) | 0.126 (0.051) | 1.161 (1.149) |