Comparative Genomics of Vibrio vulnificus, Vibrio navarrensis, and Vibrio cidicii Reveals Taxonomic Boundaries and Divergent Virulence Mechanisms

Vibrionaceae are a diverse family of bacteria that contain pathogenic species, including those within the Vulnificus clade: Vibrio vulnificus, Vibrio navarrensis, and Vibrio cidicii. While V. vulnificus is a generally well characterized environmental pathogen, V. cidicii and V. navarrensis are relatively rare, recently identified species that our current understanding of virulence and environmental adaptation is limited. Here, we investigate genetic relatedness across these three species to identify shared and species-specific genes, including markers of virulence using publicly available genome assemblies. We evaluated phylogenetic and genomic diversity across this clade by sampling all available V. navarrensis and V. cidicii genomes, and a biodiverse curated set of four V. vulnificus ecotypes to ensure representative coverage. Our results indicate that all three species share 2,321 universally conserved genes, many of which are core bacterial functions. Moreover, V. cidicii and V. navarrensis have extensive genetic similarity between them, including average nucleotide identities >95% and 619 shared genes. Despite this similarity, they both remain more phylogenetically distant from V. vulnificus and lack key virulence genes such as rtxA, indicating alternative pathogenic mechanisms. Overall, these findings reveal that virulence potential varies across the clade and environmental adaptation potential varies between species and biotypes.