93 Host genetics help shape the rumen microbiome in beef cattle

Abstract

Abstract In this study, we investigated the degree to which host genetics shape the rumen microbiome. Complex and diverse microbial communities can alter the nutrient profile available to the animal and subsequent performance. Studies of the gut microbiome have demonstrated that host genotype influences gut microbial species composition. Therefore, microbial species composition in the rumen may be a complex trait that manifests through the convergence of host-genetics and environmental factors. To test this hypothesis, we collected rumen contents and blood samples from 586 beef cattle on different diets from two locations. The rumen samples were used to sequence the V4 region of the 16S rDNA on an Illumina MiSeq platform. Animals were genotyped with various platforms and a common set of 61,974 SNP were used to conduct a genome-wide association study (GWAS) using the microbiome (OTUs, families and phyla) as response variables. The GWAS was performed using Bayesian GBLUP fitting fixed effects of cohort (location and date), and the first 2 principle components to account for population stratification. Median posterior genomic heritability estimates were 0.110, 0.124, and 0.141 at the OTU, family and phylum taxonomic level, respectively. The top 8 1-Mb windows for OTUs, families and phyla were located on 7 different chromosomes. These regions affect the rumen microbiota in multiple ways; some (chromosome 19; position 3.0–4.0 Mb) are associated with closely related taxa (Prevotellaceae, Paraprevotellaceae, and RF16), some (chromosome 27; position 3.0–4.0 Mb) are associated with distantly related taxa (Prevotellaceae, Fibrobacteraceae, RF16, RFP12, S24-7, Lentisphaerae, and Tenericutes) and others (chromosome 23; position 0.0–1.0) controlling both related and unrelated taxa. Overall, the 8 regions identified control 11 different families and 6 different phyla. This study shows that host genetics can affect rumen bacterial community members and points towards the possibility that genomics can be used to manipulate the rumen microbiome.