The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions

Abstract

Background: Bovine Digital Dermatitis (BDD) is a prevalent infectious disease, causing painful foot skin lesions and lameness in cattle. The polymicrobial nature of this disease has led to the hypothesis that the foot skin microbiota may be associated with occurrence and progression of lesions. We describe herein the bovine foot skin microbiota using 16S rRNA gene amplicon and shotgun metagenomic sequencing on samples from 259 dairy cows from three UK dairy farms. Results: We show differences in the foot skin microbiome profiles of clinically healthy animals that were associated with subsequent development of BDD. We also present the first co-occurrence analysis of the bovine foot skin microbiome. Taxonomical and functional differences together with alterations in ecological interactions between bacteria in the normal foot skin microbiome may predispose an animal to develop BDD lesions. Using genome-wide association and regional heritability mapping approaches, we provide first evidence for interactions between host genotype and certain members of the foot skin microbiota. We show the existence of genetic variation in the relative abundance of Treponema spp. and Peptoclostridium spp. and identify regions in the bovine genome that explain a significant proportion of this variation.Conclusions: Collectively this work shows the relevance of the bovine foot-skin microbiota to BDD. The description of host genetic control of members of the foot skin microbiota, combined with the association of the latter with BDD lesion development offer new insights into a complex relationship that can be exploited in selective breeding programmes aiming to enhance bovine foot health.