Discovery of novel treponemes associated with pododermatitis in elk ().

Pododermatitis, also known as treponeme-associated hoof disease (TAHD), presents a significant challenge to elk () populations in the northwestern USA, with spp. consistently implicated in the lesion development. However, identifying species-specific strains from these lesions is hindered by its culture recalcitrance and limited genomic information. This study utilized shotgun sequencing, genome reconstruction, and comparative genomics as a culture-independent approach to identify metagenome-assembled genomes (MATGs) from skin scraping samples collected from captive elk experimentally challenged with TAHD. The genomic analysis revealed 10 new MATGs, with 6 representing novel genomospecies associated with pododermatitis in elk and 4 corresponding to previously identified species and . Importantly, genomic signatures of novel genomospecies identified in this study were consistently detected in biopsy samples of free-ranging elk diagnosed with TAHD, indicating a potential etiologic association. Comparative metabolic profiling of the MATGs against other genomes showed a distinct metabolic profile, suggesting potential host adaptation or geographic uniqueness of these newly identified genomospecies. The discovery of novel genomospecies enhances our understanding of the pathogenesis of pododermatitis and lays the foundation for the development of improved molecular surveillance tools to monitor and manage the disease in free-ranging elk.IMPORTANCE spp. play an important role in the development of pododermatitis in free-ranging elk; however, the species-specific detection of from pododermatitis lesions is challenging due to culture recalcitrance and limited genomic information. The study utilized shotgun sequencing and genome reconstruction to identify novel genomospecies from elk with pododermatitis. The discovery of the novel species opens new avenues to develop molecular diagnostic and epidemiologic tools for the surveillance of pododermatitis in elk. These findings significantly enhance our understanding of the genomic landscape of the consortium while offering valuable insights into the etiology and pathogenesis of emerging pododermatitis in elk populations.