Island foxes and island spotted skunks exhibited the core mammalian microbiome, with the relative abundance of bacteria differing between host species and (for skunks) island populations
Gut microbial communities of island foxes and island spotted skunks contained high proportions of Firmicutes (SCZ: Fox=33.9%, Skunk=43.4%; SRI: Fox=20.8%, Skunk=56.8%) and Bacteroidetes (SCZ: Fox=26%, Skunk=24.5%; SRI: Fox=46.7%, Skunk=25.6%). Dominant classes within these phyla included Bacilli, Clostridia, and (for foxes) Erysipelotrichi (Phylum: Firmicutes); and Bacteroidia (Phylum: Bacteroidetes; Figure 4). Additional phyla with relative abundances above 1% included Actinobacteria (SCZ: Fox=3.6%, Skunk=21%; SRI: Fox=7.7%, Skunk=5.8%), Proteobacteria (SCZ: Fox=20.6%, Skunk=4.1%; SRI: Fox=13.3%, Skunk=7.1%), and Fusobacteria (SCZ: Fox=15.1%, Skunk=5.6%; SRI: Fox=9.7%, Skunk=4.3%). Dominant classes within these phyla included Actinobacteria and Coriobacteriia (Phylum: Actinobacteria); Gammaproteobacteria, Epsilonproteobacteria, and Deltaproteobacteria (Phylum: Proteobacteria); and Fusobacteriia (Phylum: Fusobacteria; Figure 4). All additional phyla summed to less than 2% within each island population (SCZ: Fox=0.8%, Skunk=1.4%; SRI: Fox=1.8%, Skunk=0.4%).
While the presence of taxa was largely consistent across species and islands, their relative abundances often differed. We therefore used ANCOM to identify significantly differentially abundant taxa within each island and species at the class level (Table 2). Within-island comparisons between island foxes and island spotted skunks returned four unique classes. On Santa Cruz Island, island foxes harbored more Gammaproteobacteria (W=54; 13.8% vs. 0.8%) and Deltaproteobacteria (W=50; 0.4% v. 0.009%) than island spotted skunks, while island spotted skunks harbored more Actinobacteria (W=52; 9.2% vs. 1.9%) than island foxes. On Santa Rosa Island, island foxes again harbored more Gammaproteobacteria (W=55; 9.9% vs. 0.4%) and Deltaproteobacteria (W=57; 1% v. 0.01%) than island spotted skunks, whereas island spotted skunks exhibited more Epsilonproteobacteria (W=54; 6.5% vs. 2%). Similar analyses conducted within each species revealed island-specific differences within island spotted skunks but not within island foxes (Table 2). Island spotted skunks exhibited a higher percentage of Coriobacteriia (W=54; 11.8% vs. 0.08%) on Santa Cruz Island, with no classes significantly more abundant in Santa Rosa Island skunks.