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Bovine digital dermatitis (DD) is the most important infectious disease associated with lameness in cattle worldwide. Since the disease was first described in 1974, a series of  Treponema  species concurrent with other microbes have been identified in DD lesions, suggesting a polymicrobial etiology. However, the pathogenesis of DD and the source of the causative microbes remain unclear. Here we characterized the microbiomes of healthy skin and skin lesions in dairy cows affected with different stages of DD and investigated the gut microbiome as a potential reservoir for microbes associated with this disease. Discriminant analysis revealed that the microbiomes of healthy skin, active DD lesions (ulcerative and chronic ulcerative) and inactive DD lesions (healing and chronic proliferative) are completely distinct.  Treponema denticola ,  Treponema maltophilum ,  Treponema medium ,  Treponema putidum ,  Treponema phagedenis  and  Treponema paraluiscuniculi  were all found to be present in greater relative abundance in active DD lesions when compared with healthy skin and inactive DD lesions, and these same  Treponema  species were nearly ubiquitously present in rumen and fecal microbiomes. The relative abundance of  Candidatus Amoebophilus asiaticus , a bacterium not previously reported in DD lesions, was increased in both active and inactive lesions when compared with healthy skin. In conclusion, our data support the concept that DD is a polymicrobial disease, with active DD lesions having a markedly distinct microbiome dominated by  T .  denticola ,  T .  maltophilum ,  T .  medium ,  T .  putidum ,  T .  phagedenis  and  T .  paraluiscuniculi . Furthermore, these  Treponema  species are nearly ubiquitously found in rumen and fecal microbiomes, suggesting that the gut is an important reservoir of microbes involved in DD pathogenesis. Additionally, the bacterium  Candidatus Amoebophilus asiaticus  was highly abundant in active and inactive DD lesions.

Altered Microbiomes in Bovine Digital Dermatitis Lesions, and the Gut as a Pathogen Reservoir