Table 3 Listing of the most prevalent genera in caecal samples accounting for more than 1% of sequence in one or more samples
| Â | Â | Â | Conventional | Furnished | Aviary | |||
|---|---|---|---|---|---|---|---|---|
Class | Family | Genus | Before inoculation (%)a | 4 Weeks PI (%) | Before inoculation (%) | 4 Weeks PI (%) | Before inoculation (%) | 4 Weeks PI (%) |
Bacteroidia | Rikenellaceae | Alistipes | 2.3 | 1.1 | 1.4 | 1.7 | 1.4 | 1.2 |
| Â | Bacteroides | Bacteroides | 1.4 | 1.4 | 5.3 | 4.8 | 6.2 | 5.6 |
| Â | Bacteroidaceae | Bacteroides | 2.1 | 2.5 | 0.7 | 2.1 | 1.7 | 2.6 |
| Â | Porphyromonadaceae | Barnesiella | 1.2 | 3.1 | 1.1 | 2.0 | 2.3 | 1.4 |
| Â | Porphyromonadaceae | Butyricimonas | 28.8 | 20.6 | 12.4 | 14.7 | 13.8 | 18.8 |
| Â | Porphyromonadaceae | Parabacteroides | 2.8 | 4.4 | 4.9 | 5.4 | 4.6 | 3.8 |
| Â | Â | Unclas. Bacteroidales | 4.4 | 9.8 | 9.0 | 7.1 | 10.3 | 8.9 |
| Â | Â | Unclas. Bacteroidales | 0.7 | 2.6 | 2.1 | 3.0 | 4.9 | 2.5 |
| Â | Â | Unclas. Bacteroidales | 0.2 | 2.0 | 1.0 | 2.5 | 1.0 | 1.9 |
| Â | Â | total for class | 43.8 | 47.4 | 37.8 | 43.1 | 46.2 | 46.6 |
Clostridia | Clostridiales | Blautia | 0.6 | 0.4 | 1.3 | 0.5 | 1.1 | 0.4 |
| Â | Ruminococcaceae | Faecalibacterium | 18.6 | 11.6 | 13.6 | 19.0 | 16.7 | 13.9 |
| Â | Veillonellaceae | Phascolarctobacterium | 4.3 | 0.9 | 2.6 | 0.4 | 1.8 | 3.8 |
| Â | Ruminococcaceae | Subdoligranulum | 0.0 | 0.2 | 1.4 | 1.6 | 0.9 | 0.4 |
| Â | Â | total for class | 23.6 | 21.0 | 19.0 | 22.0 | 20.0 | 23.0 |
Bacilli | Lactobacillaceae | Lactobacillus | 3.8 | 0.4 | 0.3 | 0.1 | 0.2 | 0.1 |
| Â | Lactobacillaceae | Lactobacillus | 2.3 | 4.8 | 5.4 | 2.5 | 1.9 | 5.0 |
| Â | Â | total for class | 6.1 | 5.3 | 5.7 | 2.5 | 2.1 | 5.1 |
Betaproteobacteria | Alcaligenaceae | Sutterella | 1.5 | 1.1 | 0.5 | 0.7 | 0.3 | 0.6 |
| Â | Alcaligenaceae | Sutterella | 1.1 | 0.8 | 0.6 | 0.9 | 0.6 | 0.8 |
| Â | Â | total for class | 2.6 | 1.9 | 1.1 | 1.6 | 0.9 | 1.4 |
Fusobacteria | Fusobacteriaceae | Fusobacterium | 2.2 | 1.3 | 2.4 | 1.5 | 1.8 | 0.1 |
Actinobacteria | Coriobacteriaceae | Olsenella | 1.7 | 3.9 | 1.8 | 1.4 | 0.4 | 1.9 |
Deferribacteres | Deferribacteraceae | Mucispirillum | 0.9 | 1.7 | 2.0 | 1.8 | 1.5 | 1.9 |
Epsilonproteobacteria | Helicobacteraceae | Helicobacter | 0.5 | 0.6 | 3.6 | 0.6 | 0.5 | 0.8 |
Synergistia | Synergistaceae | Cloacibacillus | 0.9 | 2.0 | 1.1 | 1.0 | 1.3 | 1.0 |
Alphaproteobacteria | Â | Unclas. Alphaproteobacteria | 0.2 | 0.1 | 1.6 | 0.5 | 0.3 | 0.4 |
Unclas. Bacteria | Â | Unclas. Bacteria | 0.2 | 0.6 | 2.6 | 2.0 | 2.0 | 1.5 |
Unclas. Firmicutes | Â | Unclas. Firmicutes | 1.1 | 0.7 | 0.6 | 1.1 | 1.1 | 0.6 |