It should be noted that most (> 92%) of the Kinase Inhibitor Library order Neisseriaceae could not be assigned at the genus level. Figure 3 Relative distribution of the ten most abundant genera identified. The distribution of genera in each individual pig, as well as the group totals are shown. Species level structure of tonsillar communities We utilized a pairwise distances program to compare the 454 16S sequences from each pig to the V4 (variable region 4) regions of the type strains for species in the families Pasteurellaceae and Streptococcaceae. Using a 97% cutoff, we determined the closest affiliation for each sequence. Sequences with closest affiliations

to Actinobacillus indolicus, A. minor, “”A. porcitonsillarum”", and Haemophilus Z-IETD-FMK ic50 parasuis were found in all samples. Sequences with closest affiliation to A. porcinus, A. rossii, H. felis, Pasteurella aerogenes, P. canis, P. multocida, and Streptococcus suis were found in most samples. Finally, sequences with closest affiliation to S. plurextorum, A. lignieresii, and A. seminis were found in small numbers in 40% of the samples. Comparison of Herd 1 time 1 and time 2 communities To determine whether the microbial communities in a given swine herd change over time, we compared the communities in tonsil tissue from pigs from Herd 1 sampled two years apart, in 2007 (time check details 1) and 2009 (time 2). Overall, the

core microbiome of the two groups of samples remained quite similar at the phylum, class, order, and family levels, with the exception that Neisseriales were more frequently identified at time 2 (10.1%

of the total) than time 1 (0.6%) (Additional file 3) and Lactobacillaceae were more common at time 1 (7.8% of the total) than time 2 (0.04%) (Additional Sinomenine file 4). Both were dominated by Pasteurellaceae, which comprised 64.2% of the total at time 1 and 50.3% at time 2 (Additional file 4). The distribution of the top ten genera was very similar, with the exception that Lactobacillus was much more common at time 1 than time 2 (Figure 3). Both groups of samples also contained the genera Treponema (phylum Spirochaetes) and Chlamydia (phylum Chlamydiae), with higher numbers of both seen at time 2. In addition, all Herd 1 time 1 samples also contained the genus Pelosinus (family Veillonellaceae), which averaged 2.3% of the total in Herd 1 time 1 but was not found at time 2 (Additional file 5). No genus present in most animals in the sample were identified as unique to Herd 1 time 2. There were no significant differences between the clusters at a 97% cutoff aligned to species of Pasteurellaceae and Streptococcaceae identified in the two groups of Herd 1 samples. There were a variety of organisms associated with soil and water, such as Polynucleobacter, Geobacter, and Azoarcus, that were found only in Herd 1 at time 1, and generally only in one or two animals (Additional file 5).