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

Abstract

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. IMPORTANCEVibrio species are important environmental aquatic bacteria that pose a threat to human and animal health across the globe. This study applied comparative genomics to investigate the genetic relatedness of Vibrio vulnificus, Vibrio navarrensis, and Vibrio cidicii, with special focus on genes associated with environmental adaptation and virulence between and within each species. Results indicate V. navarrensis and V. cidicii share many genes and are phylogenetically close, and that they possess different virulence potential than V. vulnificus. This adds to our understanding of genetic diversity and pathogenic mechanisms within an important group of marine pathogens.