Herd 2 showed the greatest variability across the four pigs sampled ranging from 197 to 730 OTUs. Pigs from Herd 1, regardless of sampling time or method, had less diversity and variation across pigs (57-251 OTUs). The first sampling that compared Herd 1

with Herd 2 had roughly twice as many sequences in Herd 2 as in Herd 1 (99,894 vs 54,932). However, the number of detected OTUs and Chao 1-estimated OTUs of Herd 2 were 3.3 and 4 fold greater than those of Herd 1. This could be seen in the rank abundance curves (data not shown) where Herd 2 had greater asymmetry (less even) and a longer tail comprised of OTUs with small Gamma-secretase inhibitor EPZ-6438 supplier populations. Table 2 Diversity and richness of the tonsillar microbial communities   # Reads # OTUsa Chao-1b Shannonc Simpsond Simpson evennesse Pig E 43770 582 980 3.14 0.10 0.02 Pig F 11386 197 268 3.40 0.07 0.07 Pig G 16519 485 820 3.73 0.05 0.04 Pig H 28219 730 1224 3.42 0.11 0.01 Herd 2 Time 1 99894 1525 2513 3.58 0.06 0.01 Pig A 12268 128 161 2.37 0.21 0.03 Pig B 14885 190 235 3.17 0.09 0.05 Pig C 9392 182 237 2.81 0.14 0.04 Pig D 18387 135 291 3.23 0.07 0.11 Herd 1 Time 1 54932 453 628 3.23 0.07 0.03 Pig J 5523 122 191 3.26 0.07 0.12 Pig K 2760 67 88 2.70 0.11 0.14 Pig L 6295 167 233 3.12 0.09 0.06 Pig M 1351 57 87 2.45 0.15 0.11 Herd 1 Time 2 15929 273 382 3.23 0.08 0.05 Pig J Brush 13361 155 228 2.04 0.29 0.02 Pig K Brush 5672 102 141 2.38 0.14 0.07 Pig L Brush 9380 251 465 2.35 0.26 0.01 Pig M Brush 11265 136 164 2.83 0.11 0.06 Herd 1 Brush 39678 418 650 2.53 0.18 0.01 a number of OTUs (based on 0.03 cut-off) found in each sample or herd b the estimated richness of an environment based on 0.03 cut-off c computed at the RDP Pyrosequencing Pipeline d calculated with MOTHUR PD184352 (CI-1040) [21] using a distance

matrix computed at RDP Pyrosequencing Pipeline e derived from Simpson’s Index where E = (1/D)/S, D is the Simpson’s Index and S is the total number of species (OTUs) Phylum, class, and order level structure of the tonsillar communities We found members of 17 different phyla of bacteria in one or more tonsil specimens examined (Additional file 1). Microbial communities in all pigs in all four groups of samples were dominated by Proteobacteria, which averaged 73.4% of the communities (ranging from 47.0% to 94.5% in individual specimens); Firmicutes, which averaged 17.8% (ranging from 3.1% to 45.6%); and Fusobacteria, which averaged 5.6% (ranging from 0.6% to 16.3%) of the total reads assigned.