Genomes of Capnocytophaga spp. and support for C. canis as a novel species

Species of the Capnocytophaga genus are commensal organisms that are most commonly found as naturally occurring flora in human, dog, and cat oral cavities. They are fastidious organisms, characterized by gliding motility and... [ view full abstract ]

Species of the Capnocytophaga genus are commensal organisms that are most commonly found as naturally occurring flora in human, dog, and cat oral cavities. They are fastidious organisms, characterized by gliding motility and grow best in an environment of 5-10% CO₂ (capnophilic) at 37^oC. Six of the eight recognized species are associated with periodontal disease in humans. C. canimorsus and C. cynodegmi inhabit the oral cavities of cats and dogs, and have the potential to become zoonotic pathogens when a human obtains a wound from a bite. Complications from bite wound infections range from sepsis to meningitis and endocarditis. These types of infections are often fatal to immunocompromised humans. In this study, we selected 10 clinical isolates from infections associated with dog bite wounds, to evaluate their taxonomic standing and to identify distinguishing features of these isolates. With 10 kbp libraries, we sequenced each genome using a PacBio RS II with the SMRTbell Template Prep Kit 1.0 and Polymerase Binding Kit P6 version 2. Paired-end sequencing (2x250 bp) was performed on NEBNext Ultra DNA libraries with an Illumina MiSeq. Canu, Pilon, and MapSolver software were used to generate complete or near complete genomes for subsequent comparative analyses. Type strain genomes, as well as representative genomes of other Capnocytophaga species deposited in NCBI, were used to determine hierarchical clustering of average nucleotide identity (ANI) distances. The clustering, within the branch containing C. canimorsus, C. canis, and C. cynodegmi, reveals a clear distinction between isolates from each species. The species C. canis was recently proposed, and we find supporting genomic and biochemical evidence for this taxon as being a distinct species.