The dominating classes were Bacteroidia and Clostridia (Figure 3), and BKM120 in vivo within these classes were Butyricimonas spp. All samples had a relatively high number of Bacteroidetes, with the exception of CC where a drop was observed in samples collected 4 weeks post infection (PI). Table 3 Listing of the most prevalent genera in caecal samples accounting for more than 1% of sequence in one or more samples       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   Bacteroides Bacteroides 1.4 1.4 5.3 Selleck ATR inhibitor 4.8 6.2 5.6   Bacteroidaceae Bacteroides 2.1 2.5 0.7 2.1 1.7 2.6   Porphyromonadaceae Barnesiella 1.2 3.1 1.1 2.0 2.3 1.4   Porphyromonadaceae Butyricimonas 28.8 20.6 12.4 14.7 13.8 18.8   Porphyromonadaceae Parabacteroides 2.8 4.4 4.9 5.4 4.6 3.8     Unclas. Bacteroidales 4.4 9.8 9.0 7.1 10.3 8.9     Unclas. Bacteroidales 0.7 2.6 2.1 3.0 4.9 2.5     Unclas. Bacteroidales 0.2 2.0

1.0 2.5 1.0 1.9     total for class 43.8 47.4 37.8 43.1 46.2 46.6 Clostridia BIIB057 Clostridiales Blautia 0.6 0.4 1.3 0.5 1.1 0.4   Ruminococcaceae Faecalibacterium 18.6 11.6 13.6 19.0 16.7 13.9   Veillonellaceae Phascolarctobacterium 4.3 0.9 2.6 0.4 1.8 3.8   Ruminococcaceae Subdoligranulum 0.0 0.2 1.4 1.6 0.9 0.4     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   Lactobacillaceae Lactobacillus 2.3 4.8 5.4 2.5 1.9 5.0     total for class 6.1 5.3 5.7 2.5 2.1 5.1 Betaproteobacteria Alcaligenaceae Sutterella Thymidine kinase 1.5 1.1 0.5 0.7 0.3 0.6   Alcaligenaceae Sutterella 1.1 0.8 0.6 0.9 0.6 0.8     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   Unclas. Alphaproteobacteria 0.2 0.1 1.6 0.5 0.3 0.4 Unclas. Bacteria   Unclas. Bacteria 0.2 0.6 2.6 2.0 2.0 1.5 Unclas. Firmicutes   Unclas. Firmicutes 1.1 0.7 0.6 1.1 1.1 0.6 a) Percentages are presented as the relative distribution compared to all OTU’s in the sample. Figure 3 Taxonomic distribution of bacterial classes in caecum.