Genus-wide re-speciation of Corynebacterium and genomic characterisation of 87 sinus isolates resolves taxonomic conflicts and identifies four candidate novel species

Abstract

Corynebacterium species are common members of the sinonasal microbiome and have shown conflicting associations with sinus health and chronic rhinosinusitis (CRS) in genus-level surveys. To better resolve the taxonomy and species-level functions of sinus corynebacteria, we generated complete long-read genome assemblies for 87 isolates, sourced from the middle meatus of 71 patients (51 with CRS, 20 healthy controls). We re-derived species boundaries de novo across the whole genus by average nucleotide identity (ANI), clustering 4,661 quality-filtered genomes retrieved from public databases and delineating higher-order species complexes. Our re-speciation assigned a species to 282 unlabelled corynebacteria, and corrected taxonomy for 266 NCBI accessions. We identified four novel candidate species from our isolate collection, and 39 public genomes fell within these species' boundaries. Whole-genome assignment reclassified 41 of our 87 isolates relative to mass-spectrometry (MALDI-TOF MS) identification, which only resolved to the species-complex level. Comparison of genome annotation characterised accessory functions that partitioned along species-complex lines, including glycogen and glycan utilisation, fatty-acid biosynthesis, cofactor (biotin and thiamine) auxotrophy, and iron-acquisition systems. Virulence and antimicrobial-resistance determinants were sparse, and the diphtheria toxin gene was universally absent. Acquired antimicrobial resistance was enriched on plasmids, whilst virulence genes were depleted from horizontally transferred compartments. Contrary to its frequent report in sinus microbiome studies, no C. tuberculostearicum genome publicly accessible via NCBI was found to be isolated from the sinonasal tract. Continued genome-level interrogation of Corynebacterium and contribution of sinus-commensals to reference databases will improve species-level understanding of the role of corynebacteria in the sinonasal microbiome.