However, the number of check details detected OTUs and Chao 1-estimated OTUs of Herd 2 were 3.3 and 4 fold greater than those of Herd 1. The Shannon and Simpson’s Diversity Indices reflected the trends seen with detected and estimated richness, with Herd 2 measurably more diverse than 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 selleck compound this website populations. The Simpson’s evenness measurement indicated that all communities were quite uneven (1.0 = perfect evenness) but that the second sampling
of Herd 1 derived from extracted tissue was less skewed than other communities. 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 Lenvatinib in vivo [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. Together, the Proteobacteria, Firmicutes, and Fusobacteria comprised 96.8% (ranging from 87.5% to 99.