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.