Markers associated with metabolome, and microbiome measures in a grain and sugar challenge in dairy heifers

Abstract Text: The aim of this preliminary study was to identify associations between the bovine genome, metabolome, and microbiome in cattle subjected to a grain and sugar challenge. The objective was to identify markers for ruminal acidosis. Genome wide association was performed on Holstein heifers (n = 34 samples with quality DNA out of 40) that were allocated to 5 feed additive groups. Heifers were fed twice daily a 62% forage:38% concentrate total mixed ration at 1.25% of bodyweight (BW) dry matter (DM)/d for a 20-d adaptation period with their additive(s). Fructose (0.1% of BW/d) was added to the ration for the last 10 d of adaptation. On d-21 heifers were challenged with a ration consisting of 1.0% of BW DM wheat and 0.2% of BW fructose plus their additive(s). Stomach tube rumen samples were collected weekly and at 5 time points over 3.6 h after consumption of the challenge ration on d-21 and analyzed for pH, and ammonia, D- and L-lactate, and volatile fatty acids (VFA) concentrations and relative abundance of total bacteria and archaea using an Illumina MiSeq platform. All rumen fermentation measures were normalized and combined to produce an eigenvector to indicate the risk of ruminal acidosis. Bovine DNA was sequenced using the Geneseek® Genomic Profiler Bovine 150K Illumina SNPchip. Genome wide association was completed using an additive model and linear regression with PCA population stratification and a Bonferroni correction for multiple comparisons. There were few genome associations found with rumen pH, acetate, propionate, total VFA, or ammonia concentration or the relative abundance of the Firmicutes and Bacteroidetes phyla (P < 0.5). A number of associations occurred for D-lactate, L-lactate, and total lactate concentration and the acidosis eigenvectors at all time points before d 21 (P < 0.05). Ten associations were found at one-time point only for butyrate and valerate concentrations (P < 0.05). A number of associations were found with the Actinobacteria, Chloroflexi, Euryarchaeota, Fibrobacteres, Proteobacteria, and Tenericutes phyla at one or more time points (P< 0.05). Gene-wide associations with the metabolome and microbiome were present despite the small population size and suggest the presence of markers for ruminal acidosis. Qualitative trait loci and candidate gene analysis is being conducted.

Keywords: genome wide association, lactic acid, ruminal acidosis