Resource-polyphenism—developmental plasticity leading to alternative adaptive trophic phenotypes (eco-morphs)—offers an exciting opportunity to explore how host physiology, gene expression, and the external environment affect the microbiome. We examined microbiome divergence between co-occurring omnivore and carnivore eco-morphs of spadefoot toad larvae in natural populations. Utilizing Illumina™ (MiSeq) sequencing and terminal restriction fragment length polymorphism (TRFLP) analyses, we assessed bacterial community structure of gut microbiome samples from 165 larvae from two populations of Spea multiplicata in Arizona and two populations of S. bombifrons in New Mexico collected in 2014. Additionally, we collected gut and skin microbiome samples from 58 larval S. multiplicata from two additional populations in Arizona in 2015. We used non-metric multidimensional scaling (NMDS) and permutation-based nonparametric multivariate analysis of variance (PERMANOVA) to assess bacterial composition between species, trophic eco-morphs, and developmental stages.
TRFLP and Illumina MiSeq provided qualitatively similar assessments of bacterial composition between groups. We found that 1) alpha diversity of gut bacterial composition was dependent upon developmental stage and eco-morph of the host, 2) beta diversity of gut bacterial community composition was influenced by an interaction between host species, eco-morphology, and developmental stage, and 3) gut and skin bacterial community composition, as predicted by eco-morph, differed between populations indicating possible influences of host genes and/or the external environment on this host-symbiont relationship. Together, our findings indicate Spea larvae are a promising new system for exploring how host development, gene expression and the environment interact to affect host-associated bacterial communities, and how host-associated bacterial communities contribute to host fitness and adaptation.