Diversity and Abundance
Three independent measures of alpha diversity (observed number of ASVs, the Shannon Diversity Index, and the Simpson Index) were largely congruent and revealed no significant differences in alpha diversity between body sites (Fig. 3). Samples from different body sites (i.e. sample types) were then combined to investigate beta diversity of the data as a whole (Fig. 4). For this combined dataset, samples were pruned and rarefied to 4,030 sequences resulting in a comparison among 606 blood samples, 353 buccal samples, 369 cloacal samples, 213 intestines samples, and 45 gizzard samples for a total of 1586 samples. Sample type significantly explained the variation of the microbiomes in both metrics tested (both p =0.001) but the variation explained varied: unweighted UniFrac R2 = 6.7%, weighted UniFrac R2 = 17%.
To assess differential abundance of microbial taxa between body sites, we conducted pairwise comparison of individual sites (excluding liver and spleen due to low sample counts), rarefying to the lower value of rarefaction between each of the two sample types being compared in each case. Overall, 56 genera were differentially abundant across all comparisons (Fig. 5, 6).