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. We describe herein the bovine foot skin microbiota and its associations with BDD using 16S rRNA gene amplicon and shotgun metagenomic sequencing on samples from 259 dairy cows from three UK dairy farms. Results We show evidence of dysbiosis, and differences in taxonomy and functional profiles in the bovine foot skin microbiome of clinically healthy animals that subsequently develop BDD lesions, compared to those that do not. Our results suggest that 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 significant 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 early changes in taxonomic and functional profiles of the bovine foot-skin microbiota in clinically healthy animals which are associated with subsequent development of BDD and could be relevant to prevention of disease. The description of host genetic control of members of the foot skin microbiota, combined with the association of the latter with BDD development offer new insights into a complex relationship that can be exploited in selective breeding programmes.

Mendelian randomization analysis of 34,497 German Holstein cows to infer causal associations between milk production and health traits

“…Another potentially mediating variable is the gut microbiome. An effect of the gut microbiome on the immune system [ 41 ], udder [ 42 , 43 ] and claw health [ 44 ] has already been mentioned by several studies. In addition, Monteiro et al [ 45 ] reported an association between the level of milk production and the microbiome of the rumen as well as of the lower gut.…”

Genetic parameters of sole lesion recovery in Holstein cows

“…One possible explanation for the delayed recovery of sole ulcers is the development of complicating secondary infections with bacteria such as treponemes, which are more frequently associated with bovine digital dermatitis ( Evans et al, 2011 ; Sykora et al, 2015 ). This complication could conceivably have a genetic background because genotype has been associated with the microbiome of chronic wounds in humans ( Tipton et al, 2020 ) and foot skin microbiome in cattle ( Bay et al, 2021 ). Another possible mechanism for genetic influence on sole lesion recovery is via IGF-1, which is a major promoter of wound healing ( Garoufalia et al, 2021 ).…”

Exploring the Influence of Growth-Associated Host Genetics on the Initial Gut Microbiota in Horses

“…Subsequent experiments have shown that A. muciniphila, a main contributor of ornithine lipids within the gastrointestinal system, supports its immunomodulatory effects. In another study, genome-wide significant variants and heritability estimates of bacteria yielded initial evidence of the interplay between cattle genotypes and skin bacteria of the foot [12]. Nevertheless, a few studies have found that diet and environmental conditions influence gut microbiota structure more significantly than host genetics [13,14].…”