Effects of host species and environment on the skin microbiome of Plethodontid salamanders

Environmental metadata for 100 Plethodon salamanders of three species sampled in the Central Appalachian Mountains. We conducted a general descriptive analysis of the bacterial OTUs identified from the three host species (n = 100), including description of their core microbiome. Then, we examined microbiome structure<b> </b>in two subsets of the data: a co-occurring species dataset (n = 62) and an elevational dataset (n = 50). Twelve individuals were included in both analyses. <br>We characterized skin microbiome structure (alpha-diversity, beta-diversity and bacterial operational taxonomic unit [OTU] abundances) using 16S rRNA gene sequencing for co-occurring <i>Plethodon</i> salamander species (35 <i>P. cinereus</i>, 17 <i>P. glutinosus</i>, 10 <i>P. cylindraceus</i>) at three localities to differentiate the effects of host species from environmental factors on the microbiome. We sampled the microbiome of <i>P. cinereus</i> along an elevational gradient (n = 50, 700 – 1000 masl) at one locality to determine whether elevation predicts microbiome structure. Finally, we quantified prevalence and abundance of putatively anti-Bd bacteria to determine if Bd-inhibitory bacteria are dominant microbiome members. <br>Pyrosequencing runs have been deposited in the National Center for Biotechnology Information Sequence Read Archive (www.ncbi.nlm.nih.gov/sra) under accession number SUB2660574