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Title: A study on the role of the foot skin microbiome and the host's genetics in the development of lameness causing foot lesions in dairy cattle
Author: Bay, V.
ISNI:       0000 0004 7970 3680
Awarding Body: University of Liverpool
Current Institution: University of Liverpool
Date of Award: 2018
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Lameness is one of the major health and welfare problems for the global dairy cattle industry causing detrimental economic losses. Lameness has been associated with foot lesions of both infectious and non-infectious aetiology. Digital dermatitis (DD) is one of the infectious disorders and has been associated with several bacteria, particularly of the genus Treponema. The main non-infectious lameness causing claw horn disruption lesions (CHDLs); sole ulcers (SU), white line disease (WLD), and toe necrosis (TN) lesions, can be secondarily infected with DD associated bacteria. The aim of this study was to examine the role of the foot skin microbiota in the development of DD lesions, to explore the microbiota profile of complicated lameness causing lesions, and to investigate the genomic regions that are linked to lameness associated traits and foot skin microbiota profiles. A total number of 554 cows from three different farms were genotyped in the study. Foot skin swabs were collected from 259 of these cows. Furthermore, 51 cows from ten different farms were used to examine the microbiota profiles of complicated lameness causing lesions as a pilot study. Foot microbiome profiles of lameness associated lesions were determined using 16S rRNA gene amplicon sequencing and the data were analysed using multivariate analysis approaches. Cattle genomic DNA samples were genotyped using a 50K single nucleotide polymorphism (SNP) chip, and genome-wide association (GWA) and regional heritability mapping approaches (RHM) were performed to find out genomic regions associated with lameness associated traits. The cows which did not acquire DD lesions during the study had significantly different foot skin microbiota profiles from those which acquired DD lesions. Besides different microbiota populations were also identified in different farms. DD, complicated CHDLs and interdigital phlegmon (IP) lesions were shown to have polymicrobial profiles consisting of similar anaerobes, such as Treponema spp., and Porphyromonas spp., but interdigital hyperplasia (IH) lesions were not associated with any specific bacteria. Furthermore, Treponema spp. were not observed as early colonizers in DD. Fastidiosipila spp. were shown to be associated with lameness causing lesions for the first time. In addition, lameness associated traits, including digital cushion thickness (DCT), were observed to have significant genomic variation, moderate heritability and partially oligogenic architecture. Lastly, some significant genomic regions were found to be potentially associated with the relative abundance of DD associated bacteria, namely, Treponema spp. and Peptoclostridium spp. In conclusion, lameness associated microbiota profiles revealed in this study could contribute to a better understanding of the aetiopathogenesis of lameness causing foot lesions leading eventually to improved treatment and prevention strategies. Moreover, genomic regions determined in this study could be included in cattle breeding programs.
Supervisor: Oikonomou, Georgios Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral