Limitations and future research priorities
Taken together with recent studies (15,16), our results suggest that focusing only on bacteria provides an incomplete picture of the host-associated microbiome. Granted, as in many other amphibian microbiome studies (14,38) our study presents microbes at a relatively coarse phylogenetic resolution (generally phylum level). Very large differences in ecology and environmental requirements likely exist between OTUs within these higher-order classification levels, thus the patterns we detected may change with higher-resolution taxonomic data. With advancing technology allowing for increased sequence length (e.g. , third-generation sequencing), more efficient microbiome analysis pipelines, and well-curated reference sequence databases, future cross-Domain microbiome research at higher taxonomic resolution should be prioritized.
Our results imply that host immunogenes play a role in structuring the amphibian skin microbiome. Furthermore, our network analyses suggest that there may be important interactions between bacteria and microeukaryotes that have been missed by previous microbiome studies focusing on only one microbial Domain. Given the widespread use of bacterial probiotic treatments in humans as well as in domesticated and wild animals (70–72) and the interest in expanding these strategies to wild amphibians (66), future studies should prioritize advancing our understanding of interactions between microbiome bacteria and eukaryotes.