Profiling skin-associated archaea and bacteria with 16S rRNA and cpn60 genes. cpn60

Performing universal prokaryotic profiling of microbial communities requires that the targeted phylogenetic marker has several important features. First, it must be universally present in all prokaryotes. Second, it should ideally be present in low copy number, or multiple copies should have high similarity. Third, it should contain sufficient nucleotide dissimilarity among species to be phylogenetically informative. The cpn60 gene is ideal in that it is universally present, usually contains one copy per genome, and is taxonomically informative enough to provide confident species-level classification when compared to the commonly used 16S rRNA gene. Applying the cpn60 gene to the mammalian skin microbiome has the potential to generate prokaryotic microbial profiles with increased species-level taxonomic resolution that can be used to address questions regarding host?microbe patterns, such as phylosymbiosis and co-evolution. Patterns of phylosymbiosis on mammalian skin were observed recently for Artiodactyla and Perissodactyla, using 16S rRNA genes clustered within 99% identity OTUs. Also observed from the same study was the presence of a “core” mammalian skin microbiome consisting of taxa affiliated with Staphylococcus and other genera. Although another study observed phylosymbiosis for primate skin microbiota, they identified a core primate skin microbial community where Staphylococcus members were differentially distributed among primate hosts. Both studies produced microbial profiles based on the 16S rRNA gene and OTU-based clustering and are thus less capable of species-level classification. By using the increased taxonomic resolution provided by the cpn60 gene, in combination with amplicon sequence variants (ASVs) capable of identifying individual amplicon sequences, the mammalian skin microbiota could be more thoroughly characterized and evaluated for patterns such as phylosymbiosis and co-evolution. As well, specific microbial genera present across all mammalian skin, such as those included within the family Staphylococcaceae, could be further defined to the species level to provide insight into species-level dynamics and host-microbe interactions. Finally, cpn60-based methods have yet to be applied to mammalian skin, although used previously for microbial profiling of the vagina and pig feces. Thus, profiling the mammalian skin microbiome using both the cpn60 and 16S rRNA genes could help validate the cpn60 gene for skin microbiome profiling and provide novel insight into mammalian skin microbial communities as they relate to host phylogeny.