Skin archaea are rare and uncommon members of mammalian skin microbiota. SKARCH

Limited skin-related archaea research has not yet allowed for a consensus on the prevalence of skin-associated archaea. Although previous research demonstrates that skin-associated archaea are rarely detected within human skin microbiome data, exist at relatively low abundance, and are primarily affiliated with Methanobacteriota and Halobacteriota phyla, other studies suggest that archaea are consistently detected and relatively abundant on human skin, with skin “archaeomes” dominated by putative ammonia oxidizers of the Nitrososphaeria class (Thermoproteota phylum - formerly Thaumarchaeota). Here we evaluated new and existing 16S rRNA gene sequence data sourced from mammalian skin and skin-associated surfaces, generated with two commonly used universal prokaryotic primers sets, to assess archaeal prevalence, relative abundance, and taxonomic distributions. Archaeal 16S rRNA gene sequences were detected in only 17.5% of 1,688 sample high-throughput sequence data, with most of the archaea-positive samples associated with non-human mammalian skin. Only 5.9% of human-associated skin sample datasets contained sequences affiliated with archaeal 16S rRNA genes. When detected, the relative abundance of sequences affiliated with archaeal ASVs was less than 1% for most mammalian skin samples and did not exceed 2% for any samples. Although several computer keyboard microbial profiles were dominated by Nitrososphaeria sequences, all other skin microbiome datasets tested were primarily composed of sequences affiliated with Methanobacteriota and Halobacteriota phyla. Our findings revise downwards recent estimates of human skin archaeal distributions and relative abundances, especially those affiliated with the Nitrososphaeria, reflecting a limited and infrequent archaeal presence within the mammalian skin microbiome.