Family, not phylogeny, drives microbiome differences in Oklahoma salamanders

While some previous studies of salamander skin microbial diversity indicate that phylogeny is the most important factor shaping diversity and microbial communities, others (typically focused on the genus or species level) indicate that host ecology and environment are more important drivers. Our results refine these seemingly contradictory findings from previous studies, indicating that the most important driver of salamander skin microbiomes is not phylogeny (i.e., the evolutionary distance between hosts), but specific differences between microbiomes in the salamander families Salamandridae and Plethodontidae. Once these large distinctions are accounted for no additional phylogenetic signal remains, with differences instead related to host environment and ecology. Past work has also indicated that the presence of the pathogens Batrachochytrium dendrobatidis (Bd) and ranavirus cause changes in the number and makeup of microbes present in the skin microbiome. While we found diminished microbiome diversity and differential microbial abundance related to Bd, we did not find any effect of ranavirus status.