Table 1.
Relative abundance of OTUs before and after elimination of antibiotic treatment in two different farms (>1% relative abundance).
| OTU | Relative abundance (%) | |||||
|---|---|---|---|---|---|---|
| MT1 | MT2 | P value | MC1 | MC2 | P value | |
| Acinetobacter | 1.090 | 0.835 | 0.132 | <1 | <1 | NA |
| Actinobacillus | 0.837 | 1.123 | 0.728 | <1 | <1 | NA |
| Afipia | <1 | <1 | NA | 0.000 | 1.089 | 0.001* |
| Alistipes | <1 | <1 | NA | 1.242 | 0.006 | <0.001* |
| Alloprevotella | 0.048 | 1.902 | 0.064 | 0.444 | 1.635 | 0.021* |
| Anaerovibrio | 0.011 | 1.009 | 0.037* | 0.048 | 1.094 | 0.010* |
| Bacteroides | <1 | <1 | NA | 1.694 | 0.366 | <0.001* |
| Barnesiella | 0.104 | 2.001 | 0.049* | 1.172 | 2.562 | 0.160 |
| Bergeyella | 23.275 | 4.370 | 0.003* | 8.215 | 0.009 | <0.001* |
| Bosea | <1 | <1 | NA | 0 | 1.153 | <0.001* |
| Campylobacter | 0.007 | 1.883 | 0.021* | 0.030 | 2.882 | 0.001* |
| Clostridium sensu stricto | <1 | <1 | NA | 1.207 | 0.736 | 0.039* |
| Clostridium IV | <1 | <1 | NA | 2.473 | 1.283 | 0.017* |
| Clostridium XI | <1 | <1 | NA | 1.341 | 0.723 | 0.017* |
| Clostridium XlVa | <1 | <1 | NA | 2.416 | 1.195 | 0.017* |
| Escherichia/Shigella | 0.100 | 1.174 | 0.418 | 0.528 | 2.212 | 0.058* |
| Faecalibacterium | 0.026 | 1.411 | 0.011* | 0.098 | 1.633 | 0.001* |
| Gemmiger | 0.019 | 1.186 | 0.015* | <1 | <1 | NA |
| Haemophilus | 13.896 | 2.927 | 0.015* | 0.905 | 2.195 | 0.026* |
| Klebsiella | <1 | <1 | NA | 8.810 | 0.011 | <0.001* |
| Lachnospiracea_incerta_sedis | 0.068 | 1.233 | 0.132 | 0.328 | 1.089 | 0.117 |
| Lactobacillus | 0.328 | 3.453 | 0.004* | 1.400 | 4.406 | 0.032* |
| Megasphaera | 0.010 | 2.164 | 0.008* | 0.033 | 4.971 | 0.001* |
| Moraxella | 34.220 | 9.185 | 0.015* | 34.024 | 3.189 | 0.001* |
| Mycoplasma | 3.051 | 0.577 | 0.011* | 6.718 | 10.324 | 0.509 |
| Neisseria | 5.09 | 4.26 | 0.780 | 1.00 | 0.02 | 0.003* |
| Oscillibacter | 0.119 | 1.426 | 0.165 | 1.586 | 1.483 | 0.680 |
| Paraprevotella | 0.010 | 1.067 | 0.028* | 0.039 | 1.131 | <0.001* |
| Phascolarctobacterium | 0.043 | 3.013 | 0.004* | 0.106 | 4.072 | <0.001* |
| Prevotella | 0.364 | 14.066 | 0.083 | 1.319 | 16.805 | 0.002* |
| Psychrobacter | 0.276 | 5.518 | 0.563 | <1 | <1 | NA |
| Roseburia | 0.020 | 2.466 | 0.005* | 0.080 | 1.972 | 0.001* |
| Rothia | 0.558 | 1.406 | 0.817 | <1 | <1 | NA |
| Selenomonas | 0.007 | 1.113 | 0.028* | <1 | <1 | NA |
| Staphylococcus | 1.493 | 0.029 | 0.002* | <1 | <1 | NA |
| Streptococcus | 1.584 | 1.028 | 0.418 | 1.002 | 0.982 | 0.457 |
| Succinivibrio | 0.012 | 1.058 | 0.037* | 0.083 | 1.706 | 0.137 |
| Treponema | 0.047 | 2.666 | 0.105 | 0.083 | 3.554 | <0.001* |
*Significantly different.
NA, not available. When the relative abundance was <1% in both sampling times, the P value was not estimated. The OTU was included for comparison with the other farm that showed higher abundance (>1%).