The varied topography of human skin offers a unique opportunity to study how the body’s microenvironments influence the functional and taxonomic composition of microbial communities. However, the paucity of commensal microbial genomes has limited our ability to comprehensively interpret the structure and function of these communities. We combined extensive culturing and co-assembly of shotgun metagenomic datasets spanning multiple body sites of multiple individuals to elucidate novel constituents, structure and functions of the human skin microbiome.

Candida auris is an emerging multi-drug resistant fungal pathogen. C. auris skin colonization results in environmental shedding, which underlies hospital transmissions, and predisposes patients to subsequent infections. Combining culturing and skin microbiome sequencing of an outbreak at a high-acuity long term care facility provided novel insight into prevalence and site tropism for C. auris colonization.  We developed a murine skin topical exposure model for C. auris to dissect risk factors predisposing patients for colonization and to test interventions that might protect patients.