Genome-Scale Analysis Reveals Strain Kdesi as a Distinct Evolutionary Lineage and Extensive Cryptic Diversity in the Genus Bdellovibrio

Bdellovibrio are predatory bacteria with potential applications in treating multidrug-resistant bacterial infections. We isolated Bdellovibrio sp. kdesi from sewage in Reynosa, Mexico, and performed comprehensive genomic characterization. The complete genome (3,343,978bp; 48.5% GC content; 3,208 coding sequences) contains a single rRNA operon with two identical 16S rRNA genes at distinct loci. While 16S rRNA analysis showed 99.3% identity to B. bacteriovorus SSB218315, polyphasic genomic analysis revealed kdesi as a distinct species. Core-genome phylogeny, average nucleotide identity (ANI ~ 89%), average amino acid identity (AAI ~ 82%), and digital DNA-DNA hybridization (dDDH < 70%) clearly demonstrated that Kdesi along with several other strains currently classified as B. bacteriovorus represents novel genomospecies requiring formal taxonomic revision. Comparative genomic analysis of 29 Bdellovibrio genomes revealed an open pan-genome (~ 25,000 genes) with limited transposable elements, absence of SecB in the Sec secretion system, and strain-specific adaptations in Type IV secretion systems. These findings underscore the need for genome-based taxonomic revision of the genus and highlight the importance of using multiple molecular criteria beyond 16S rRNA for bacterial species delineation.