High-resolution Staphylococcus profiling reveals intra-species diversity in a single skin niche

The skin microbiome is dominated by a few key genera, among which <i>Staphylococcus</i> is one of the most well characterized. Recent studies have examined the roles of various <i>Staphylococcus</i> species such as <i>Staphylococcus epidermidis</i> and <i>Staphylococcus hominis</i> within broader skin microbial communities. However, these investigations often rely on isolates from multiple individuals and hence limit their ability to capture intra-community interactions. In this study, we focused on the axillary microbiome of a single healthy individual to characterize the genetic and functional diversity of resident <i>Staphylococcus</i> isolates. Using a low-cost, high-throughput DNA extraction and long-read whole-genome sequencing pipeline, we generated complete genomes for 93 isolates spanning 7 genetically distinct lineages across 3 major skin species. These comprised one dominant and three additional lineages of <i>S. epidermidis</i>, two of <i>S. hominis</i> and one of <i>Staphylococcus capitis</i>. Functional and metabolic analyses revealed species- and strain-specific features, suggesting potential metabolic cross-feeding and specialization within this community, including within strains of <i>S. epidermidis</i>. These findings highlight the metabolic complexity and potential interdependence of staphylococci inhabiting a single skin site and the need for strain-level resolution of the community. The strains form part of the York Skin Microbiome (YSM) collection, a growing open biobank of genetically diverse skin isolates from matched individuals.