Factors driving global microbiome composition: Beta diversity
Overall, the first two PCoAs accounted for almost 40% of all variance in the Bray-Curtis distances across all samples. The clustering patterns revealed YIAL as an outlier cross, CHILL as intermediate, and the remaining stocks clustering more closely together on the axes (Figure 3). Using the overall PERMANOVA model, significant population effects were found in the overall microbial community structure using Bray-Curtis distances (p = 0.001, R2 = 0.046) (Table 3). Pairwise PERMANOVA tests using Bray-Curtis distances showed that YIAL was statistically different from BQ (p = 0.0028), CAP (p = 0.005), NIT (p = 0.005), PUNT (p = 0.005), QUIN (p = 0.0065), and RC (p = 0.005) but not from CHILL (p > 0.05), and all other pairwise PERMANOVA comparisons showed a lack of significant pairwise differences (Supplementary Table 5). In the overall PERMANOVA model, sire effects were found to have significant effects on the microbial community (p = 0.002, R2 = 0.25; Table 3). Furthermore, using a unique PERMANOVA model for each cross, sire effects on Bray-Curtis distances were found to be significant within CHILL and NIT (p = 0.001, R2 = 0.434 and p = 0.006, R2 = 0.308, respectively), but no significant sire effects were found within other crosses (Table 4). Finally, while pen effects did not contribute significantly to differences in overall microbiome community composition for Bray-Curtis distances, a significant difference was found between replicate pens for RC (p= 0.021 and R2 = 0.262, Tables 4).