Characterizing the microbiota of bovine digital dermatitis

Abstract

Bovine digital dermatitis (DD) is a skin disease affecting cattle worldwide. As a significant contributor to infectious lameness, DD is increasingly an economic and animal welfare concern for dairy and beef producers. DD is a polymicrobial disease, with many different types of anaerobic bacteria strongly associated with lesions. No causative agents or etiopathogenesis mechanisms of DD are yet accepted due to the multiple different species present and microbiota variation among individual lesions. The involvement of Treponema in lesion development is generally accepted, whereas what combination of other anaerobic bacteria are involved is currently debated. Insufficient and incomplete identification and characterization of these additional species are a limiting factor in DD pathogenesis research. This thesis aimed to fill the gaps in knowledge of these additional anaerobes throughout DD lesions, while providing the first comprehensive description of DD microbiota in feedlot beef cattle. Through high throughput sequencing and culturing of DD tissue biopsies, we identified Treponema, Mycoplasma, Fusobacterium spp., Porphyromas levii, and Bacteroides pyogenes as potential DD pathogens, and used a multiplex qPCR for absolute quantification and reproducible characterization of species population dynamics. We identified T. medium, P. levii, and T. phagedenis as a group strongly associated with early lesion stages, thus potentially being involved in lesion formation. Through a meta-analysis of all publicly available DD metagenomic studies, we identify Treponema, Mycoplasma, Fusobacterium, and Porphyromonas as the primary DD-associated microbiota. We recommend focusing future DD research efforts on culturing and characterizing species of these groups in an effort to establish etiopathogenesis mechanisms of DD.