Host habitat shapes the gut microbiomes of insular reptilian hosts in the Philippines

Abstract

Islands have long served as ideal, replicative “natural laboratories” to help identify the mechanisms that shape the diversity and distribution of plant and animal communities, and a burgeoning body of literature has utilized island-like systems to better understand the processes that shape microbial community diversity. Despite this expanded application, few studies have explored patterns of microbial diversity spanning true islands, especially among communities of microorganisms that colonize vertebrate hosts (i.e. microbiomes). Here, we use 16S ribosomal ribonucleic acid microbial inventories to elucidate the roles that host evolutionary history, host habitat, host microhabitat, and geographic location play in the assemblage of gut microbiomes among reptilian hosts spanning multiple islands in the Philippines. Host habitat and microhabitat explained most of the variation in gut microbiome diversity observed among our focal hosts. Although we identified some significant differences in microbiome diversity across two of the host suborders (Lacertilia and Serpentes) and some host families, we did not find evidence of phylogenetic signal. We also conducted analyses of microbiome diversity across various geographic scales, and found that hosts inhabiting the same island, but different localities, did not possess significantly different gut microbiomes. However, the gut microbial diversity of hosts inhabiting distinct islands were significantly different across numerous measures of microbiome diversity. Results from this robust, comparative study contribute to our growing knowledge of the host-associated and geographic mechanisms that shape the vertebrate gut microbiome and represents one of the first studies to characterize variation in gut microbial communities among vertebrate hosts inhabiting multiple Philippine islands.