Bacterial composition was significantly influenced by host species, with subtler inter-island differences more pronounced in island spotted skunks compared to island foxes
Both Bray-Curtis Dissimilarity and the Jaccard Index were significantly predicted by species, island, their interaction, and sequencing plate (adonis: Table 1). Across both beta diversity measures, species explained the largest proportion of the variance in the dataset, with 24.0% for Bray-Curtis and 19.1% for Jaccard. Principal coordinate plots mirrored this result (Figure 3 A-B), with separation by species clearly evident along PC1, which explained 24.70% of the variation for Bray-Curtis and 20.49% of the variation for Jaccard. Further examination Bray-Curtis Dissimilarity revealed separation between foxes by an unknown variable along PC2 (which explained 6.388% of the variation) and between skunks by island along PC3 (which explained 6.188% of the variation; Figure S2). Using Jaccard Distances, we observed separation between skunks by island along PC2 (which explained 5.985% of the variation) and between sequencing plates along PC3 (which explained 4.176% of the variation; Figure S2).
Given the strong influence of species on bacterial community structure, we created subsets of the data by species to look for finer-scale intraspecific differentiation between island populations. Within island spotted skunks (Figure 3 C-D), bacterial abundance and presence were significantly predicted by island (adonis: Bray-Curtis, F =10.936,R2 =0.159, df =1, p= 0.001; Jaccard,F =10.386, R2 =0.146, df =1,p= 0.001) and sequencing plate (adonis: Bray-Curtis,F =2.967, R2 =0.086, df =2,p= 0.001; Jaccard, F =4.460,R2 =0.125, df =2, p= 0.001). We observed similar patterns in island foxes (Figure 3 E-F), although island (adonis: Bray-Curtis, F =3.625,R2 = 0.063, df =1, p= 0.001; Jaccard, F =3.379, R2 =0.056, df =1,p= 0.001) and sequencing plate (adonis: Bray-Curtis,F =1.934, R2 =0.067, df =2,p= 0.002; Jaccard, F =3.254,R2 =0.109, df =2, p= 0.001) explained lower proportions of variation.