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Associations of host genotype with foot skin microbiota profiles and digital dermatitis related bacteria
Bay, V.; Sánchez-Molano, E...
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Objectives: Associations between host genetics and skin microbiota profiles have been shown in humans and mice. We have recently described the bovine foot skin microbiota using 16S rRNA amplicon and shotgun metagenomic sequencing and showed associations with the development of digital dermatitis (DD) in dairy cattle. Here we used genome wide association and regional heritability mapping approaches to provide first evidence for significant interactions between the host’s genotype and the bovine foot skin microbiota profiles.
Materials and Methods: Swabs were taken from the heel bulb region of the back-left foot of 259 cows from 3 UK farms 3-4 weeks before calving. 16SrRNA amplicon sequencing was carried out for all samples using the Illumina® HiSeq 2500 platform, and taxonomic assignment of OTUs carried out using QIIME and the RDP classifier. Chao 1, Shannon and Simpson indices were calculated to describe alpha-diversity, and weighted UniFrac distances and non-metric multidimensional scaling values were used to describe beta-diversity.
Cattle genomic DNA samples were genotyped using a 50K SNP chip. Genome wide association analyses (GWA) and regional heritability mapping (RHM) of consecutive 20 SNPs were performed to identify genomic regions associated with various diversity indices and with the relative abundance of genera found to be associated with the development of DD lesions.
Results: Host genotype was not found to be associated with the overall richness and diversity of the foot skin microbiome. However, significant associations were found between the host’s genotype and two bacterial genera associated with DD. The heritabilities for relative abundances of Peptoclostridium spp. and Treponema spp. were 0.59 ± 0.18 and 0.52 ± 0.00, respectively. One suggestive SNP on BTA6 and one significant SNP on BTA 19 were associated with relative abundance of Peptoclostridium spp. Four significant and two suggestive SNPs on BTA1, one suggestive and one significant SNP on both BTA9 and BTA17, one significant SNP on BTA16, and one suggestive SNP on BTA2, BTA6, BTA8, BTA19, BTA21 and BTA29 were associated with relative abundance of Treponema spp.
On BTA1, the region associated with relative abundance of Treponema spp. explained 9.88% of the total genomic variance and included the genes GMPS and PLCH1. GMPS encodes guanine monophosphate synthetase which plays a role in de novo synthesis of guanine nucleotides; the cyclic GMP was shown to be associated with immune signaling pathways. PLCH1 is a member of the phospholipase enzyme family that generates the secondary messengers inositol 1,4,5-trisphos- phate (IP3) and diacylglycerol (DAG) by cleaving phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2). Phospholipases were shown to be involved in inflammation mechanisms, especially the expression of PLCH1 were shown to be downregulated by lipopolysaccharides (LPS)5 which is found in the outer membrane of Gram-negative bacteria. These associations may explain the role of the genomic region on BTA1 in immune and inflammatory response against the Gram-negative Treponema infections. The region associated with relative abundance of Treponema spp. on BTA16 explains 34.78% of the total genomic variance and includes the gene PTPRC encoding a transmembrane tyrosine phosphatase which was shown to be upregulated after administration of external bacteria to the intestine of mice.
Conclusion: In the present study, DD-linked foot skin microbiome traits were investigated using GWA and RHM approaches, leading to a first understanding of the genomic architecture of these traits.
Keywords: Digital dermatitis, Microbiome, Genetics, Genomics, Lameness.
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Affiliation of the authors at the time of publication
Ege University, Faculty of Agriculture, Department of Animal Science, Turkey;
The Roslin Institute and R(D)SVS, University of Edinburgh, United Kingdom;
Institute of Infection and Global Health, University of Liverpool, United Kingdom;
Institute of Veterinary Science, University of Liverpool, United Kingdom.
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