Keynote Presentation: Comparative Genomics of Two Common Skin Microbiome Members: CoNS Staphylococcus and Corynebacterium Tuberculostearicum with Live Q&A

Human skin is characterized by a limited number of phyla including, Actinomycetota, Bacillota and Pseudomonadota. In particular, Staphylococcus (Bacillota) and Corynebacterium (Actinomycetota) are dominant genera present on the skin. While clinically relevant members of these taxa are well characterized (e.g., S. aureus), some coagulase-negative Staphylococci and non-diphtheria Corynebacteria remain under-sequenced. We analyzed 16S rRNA V1-V3 marker data from 23 healthy volunteers to identify species from these two genera that were both abundant and prevalent on healthy human skin. S. capitis, S. epidermidis and S. hominis were the dominant Staphylococcus species on skin, found on 100% of subjects. We sequenced 126 genomes from these species to fill out the taxonomic tree and build a genus-wide pangenome. The genus-core consisted of 1660 genes (21%) which included pathways with a predicted functions in skin colonization. The remaining 79% of genes in the pangenome catalog were present in only a subset of genomes and included pathways involved in amino acid and cofactor metabolism. 16S rRNA gene analysis also identified Corynebacterium tuberculostearicum at 94% of body sites and 100% of individuals. We sequenced a collection of 23 Corynebacterium genomes that, when placed in the context of a whole genome phylogenetic tree, support the hypothesis that C. tuberculostearicum is a species complex rather than a single species. In addition, we propose that four of our strains belong to a new species with a strong niche-specificity for sites on the feet. The expanded genome collection, when compared to existing public references, facilitated the mapping of 24% more C. tuberculostearicum species complex metagenomic reads across body sites and individuals. In summary, genome sequencing of four prevalent skin-associated species contributes to a more complete catalog of skin bacteria and improves our understanding of microbial diversity on the skin. 

Learning Objectives: 

1. Describe key features and taxa of the skin microbiome.

2. Discuss the functional diversity of coagulase-negative Staphylococcus on the skin.

3. Recognize genomic and pangenomic features of specialization on the skin.