Bacterial DNA on the skin surface overrepresents the viable skin microbiome

Abstract

The skin microbiome provides vital contributions to human health and was historically assumed to be a well-mixed community that coats the skin surface. However, its spatial organization and viability remain unclear. Here we apply culturing, imaging, and molecular approaches to both human and mouse skin samples, and find that the skin surface is colonized by far few viable bacteria than would be predicted by its levels of bacterial DNA. Instead, viable skin-associated bacteria are primarily present in hair follicles and other cutaneous invaginations. Furthermore, we establish that a relatively small number of bacterial families dominate each skin site and that traditional sequencing methods overestimate the skin microbiome’s richness and diversity. These findings address multiple outstanding questions in skin microbiome biology with significant implications for future efforts to study and manipulate it.