0%), Clostridiales (14.3%), Pseudomonadales (11.8%), Fusobacteriales (5.6%), Lactobacillales (3.4%), Neisseriales (2.8%) and Enterobacteriales (2.0%). In addition, the Actinomycetales

(0.9%), Burkholderiales (0.3%), and Bacteroidales (0.3%) were find more found in most animals in all groups of specimens. These ten orders form the core microbiome of porcine tonsils, and together represent 97.4% (ranging from 88.0% to 99.7% in individual specimens) of the reads assigned at the order level (Table 3). Bacillales (0.14%) and Campylobacterales (0.13%) were also found in small numbers in half of the specimens. Family and genus level structure of the tonsillar communities We found members of 61 families (Additional file 4) and 101 genera (Additional file 5) in at least one tonsil specimen. Five families were found in all pigs in all groups of specimens: Pasteurellaceae (60.2%), Moraxellaceae (12.3%), Fusobacteriaceae (5.6%), Veillonellaceae (4.4%), and Neisseriaceae (3%). In selleck compound addition, three families, the Peptostreptococcaceae (2.2%), Enterobacteriaceae (2.2%), and

Streptococcaceae (0.5%), were found in most animals in all groups of specimens. These eight families form the core microbiome in porcine tonsils, and represent 90.4% (ranging from 73.5% to 99.0% in individual specimens) of the reads assigned at the family level (Table 3). It should be noted that almost half (46.8%) of the Clostridiales could not be assigned at the family level. Of the 101 genera identified in these samples, 49 were found in both herds (Additional file 5). Thirty-seven genera represented at least 0.1% of the total reads from all specimens (Figure 2). Of these 37

genera, 13 were found Thiamine-diphosphate kinase in all 4 groups of specimens, 2 were found only in Herd 1, 1 was found only in Herd 2, and 8 were found in tissue specimens but not in brush specimens. Figure 2 Taxonomic characterization of the four groups of samples obtained by 454 pyrosequencing. Bars illustrate the proportion of reads classified into particular genera. Only genera that contain at least 0.01% of the total number of reads are shown. The relative distribution of the top ten genera found in these specimens is shown in Figure 3. These 10 genera comprised on average 88.3% (ranging from 67.2% to 98.8%) of the total genera in the microbial communities in these specimens. Actinobacillus (Pasteurellaceae), Alkanindiges (Moraxellaceae), Fusobacterium (Fusobacteriaceae), and Haemophilus (Pasteurellaceae) were found in all pigs in all groups of specimens. Pasteurella (Pasteurellaceae), Veillonella (Veillonellaceae), Peptostreptococcus (Peptostreptococcaceae), and Streptococcus (Streptococcaceae) were found in almost all pigs in all groups of specimens. These eight genera form the core microbiome in porcine tonsils, and represent 85.1% of the reads assigned to the genus level (Table 3).