Revealing the diversity of commensal corynebacteria from a single human skin site.

Abstract

Our understanding of the skin microbiome has significantly advanced with the rise of sequencing technologies. While Corynebacterium species are a major component of the human skin microbiome, research has largely centered on other prevalent genera like Staphylococcus and Cutibacterium. Prior to this study, complete genomes for skin-associated Corynebacterium were limited. For instance, only nine were available for the commonly identified species Corynebacterium tuberculostearicum. In this study, we explored Corynebacterium diversity from a single skin site, the axilla, using selective media to enrich for these bacteria. Long-read whole-genome sequencing and bioinformatic analysis of the enriched isolates provided unprecedented insight into the diversity of this genus at a single body site. The study yielded 215 closed genomes, comprising 30 distinct representative genomes following dereplication. These genomes span seven distinct species, including two new species provisionally named Corynebacterium axilliensis and Corynebacterium jamesii, as well as species not previously linked to the skin. Pangenome analysis of these isolates uncovered potential metabolic differences, antimicrobial resistance genes, novel biosynthetic gene clusters, prophages, and phage defense systems. This study represents the most detailed analysis to date of Corynebacterium from a single skin niche and highlights extensive variation even within a single host. Our culture-based Nanopore sequencing approach has expanded the number of publicly available skin Corynebacterium genomes, providing a valuable resource for future studies investigating the diversity and function of this important skin genus.

Importance: This study uncovers the hidden diversity of Corynebacterium, an important yet often overlooked group of bacteria inhabiting human skin. Focusing on the underarm and using advanced sequencing techniques, we identified over 200 complete bacterial genomes. This collection includes species not previously known to reside on the skin, as well as two entirely new species, highlighting how little is currently known about this cutaneous genus. Most of these bacteria were isolated from a single individual, underscoring the vast microbial diversity that can exist within one person. By closely examining the corynebacterial community at a single site, we begin to uncover the complex relationships within a true microbial ecosystem. These findings deepen our understanding of the skin microbiome and provide a valuable resource for future research into how these microbes affect skin health, hygiene, and disease.