Genomic characterization of the
C. tuberculostearicum
species complex, a prominent member of the human skin microbiome
Authors: Ahmed Nashwa , Joglekar Payal , Deming Clayton ,   NISC Comparative Sequencing Program, Lemon Katherine P. , Kong Heidi H. , Segre Julie A. , Conlan Sean , Barnabas Beatrice B. , Black Sean , Bouffard Gerard G. , Brooks Shelise Y. , Crawford Juyun , Marfani Holly , Dekhtyar Lyudmila , Han Joel , Ho Shi-Ling , Legaspi Richelle , Maduro Quino L. , Masiello Catherine A. , McDowell Jennifer C. , Montemayor Casandra , Mullikin James C. , Park Morgan , Riebow Nancy L. , Schandler Karen , Schmidt Brian , Sison Christina , Stantripop Sirintorn , Thomas James W. , Thomas Pamela J. , Vemulapalli Meghana , Young Alice C. 
Published: November 2023

ABSTRACT

Corynebacterium
is a predominant genus in the skin microbiome, yet its genetic diversity on the skin is incompletely characterized and underrepresented in public databases. We investigated the distribution of
Corynebacterium
species on the skin and expanded the existing genome reference catalog. We used extant V1-V3 16S rRNA gene sequencing data from 14 body sites of 23 healthy volunteers to characterize
Corynebacterium
diversity across human skin.
Corynebacterium tuberculostearicum
, recently proposed to belong to a species complex, is frequently found on human skin. We identified two distinct
C. tuberculostearicum
ribotypes (A and B) that can be distinguished by variation in the 16S rRNA V1-V3 sequence: ribotype A is distributed across all skin sites, while B is found primarily on the feet. We performed whole genome sequencing of 40
C
.
tuberculostearicum
isolates cultured from the skin of five individuals across seven skin sites. We generated five closed
C. tuberculostearicum
genomes and determined that they are largely syntenic and carry a diversity of methylation patterns, plasmids, and CRISPR/Cas systems. The pangenome of
C. tuberculostearicum
is open with a core genome size of 1,806 genes and a pangenome size of 5,451 genes. This expanded pangenome enabled the mapping of 24% more
C. tuberculostearicum
reads from skin metagenomes. We demonstrated differential growth phenotypes of
C. tuberculostearicum
ribotypes A and B on rich and skin-like media, suggesting functional differences. Finally, while the genomes from this study fall within the
C. tuberculostearicum
species complex, we propose that ribotype B isolates constitute a putative new species.

IMPORTANCE

Amplicon sequencing data combined with isolate whole genome sequencing have expanded our understanding of
Corynebacterium
on the skin. Healthy human skin is colonized by a diverse collection of
Corynebacterium
species, but
Corynebacterium tuberculostearicum
predominates on many skin sites. Our work supports the emerging idea that
C. tuberculostearicum
is a species complex encompassing several distinct species. We produced a collection of genomes that help define this complex, including a potentially new species we term
Corynebacterium hallux
based on a preference for sites on the feet, whole-genome average nucleotide identity, pangenomic analysis, and growth in skin-like media. This isolate collection and high-quality genome resource set the stage for developing engineered strains for both basic and translational clinical studies.