Microbial diversity of Appalachian salamander skin

We used 16S amplicon sequencing to profile the microbiome of Appalachian salamanders skin and the environmental microbiomes from the salamander sampling sites. We sampled 10 species of salamander (Ambystoma jeffersonianum, Desmognathus fuscus D. monticola, D. ochrophaeus, Eurycea bislineata, Gyrinophilus porphyriticus, Notophthalmus viridescens, Plethodon cinereus, P. glutinosus, P. hoffmani) at 12 sites within three localities in Maryland and Virginia, USA. We amplified the V3-V5 region of the 16S rRNA gene (~380 bp) using the universal primers 515F-Y and 939R, and sequenced the libraries on two Illumina MiSeq runs. We used the data to quantify the effects of host phylogeny, environmental microbial diversity climate and geographic distance on microbiome structure.