Comparative and phylogenomic analysis of Eikenella genus suggest taxonomic reclassification of Eikenella corrodens strain KCOM 3110 as novel species and reveals unique CE1 carbohydrate-active enzyme family.

The Eikenella genus includes opportunistic pathogens of clinical importance, commonly associated with infections such as endocarditis, periodontitis, wound abscesses, and respiratory tract infections; however, its taxonomy, genetic diversity, and evolutionary relationships remain poorly understood. This study aims to clarify the genomic diversity and taxonomic boundaries within the genus through comprehensive comparative and phylogenomic analyses. We conducted a genomic comparison of 63 Eikenella genomes, including 35 high-quality drafts and 5 complete genomes, to understand their phylogenetic relationships and identify potential taxonomic misclassifications. Notably, Eikenella corrodens strain KCOM 3110 had the largest genome (2.46 Mb), the highest number of CDSs (2,877), and carried 611 unique genes among complete Eikenella strains. Phylogenetic trees based on 16S rRNA and whole genome data showed that KCOM 3110 did not cluster with the Eikenella corrodens group, but was closer to Eikenella halliae. The average nucleotide identity (~ 93%) and digital DNA-DNA Hybridization (~ 51.7%) values with Eikenella corrodens were below the species-level thresholds. Importantly, unique genes for antimicrobial resistance, metal tolerance, phage functions, and a distinct CE1 CAZyme profile supported its novelty. Overall, these findings indicate that Eikenella corrodens strain KCOM 3110 represents a novel species within the Eikenella genus. The study highlights the power of genome-based approaches in resolving bacterial taxonomy. It provides new insights into the evolutionary and functional diversity of Eikenella while laying the foundation for future studies on the ecological role, pathogenic potential, and clinical significance of this novel species.