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).