Holstein heifers (n = 40) were allocated to 5 groups: (1) control; (2) virginiamycin (10 g/d); (3) monensin (2.2 g/d) + tylosin (0.44 g/d); (4) monensin (2.5 g/d) + yeast (Levucell SC Direct 25 g/d); (5) sodium bicarbonate (200 g/d) + magnesium oxide (30 g/d). Heifers were fed a 62% forage:38% concentrate total mixed ration for a 20-d adaptation with their additive(s). Fructose [0.1% of bodyweight (BW)/d] was added for the last 10 d of adaptation. On d-21 heifers were fed with 1.0% of BW dry matter wheat and 0.2% of BW fructose plus additive(s). Rumen samples were taken weekly and 5 times over 3.6 h after challenge and analyzed for pH, and ammonia, D- and L-lactate, and VFA concentrations. Relative abundance of bacteria and archaea were determined using Illumina MiSeq. Rumen metabolites were analyzed to produce an eigenvector that indicates the risk of ruminal acidosis. The DNA was sequenced using the Geneseek Genomic Profiler Bovine 150K Illumina SNPchip from 34 heifers. Genome-wide association used an additive model and linear regression with PCA population stratification and a Bonferroni correction for multiple comparisons. Few genome associations were found with rumen pH, acetate, propionate, total VFA, or ammonia concentration or relative abundance of Firmicutes and Bacteroidetes phyla pre-challenge or challenge. Metabolites and microbial phyla that had associated markers and genomic regions identified were: acetate:propionate (A:P), D-, L-, and total lactate, butyrate, acidosis eigenvector, Actinobacteria, Chloroflexi, Archaea, Fibrobacteres, Proteobacteria, and Tenericutes. A putative genomic region overlapped for Actinobacteria, Archaea, and Fibrobacteres and the region that codes for matrix extracellular phosphoglycoprotein. Other overlapping regions were found for: (1) Chloroflexi, Tenericutes, and A:P, (2) L- and total lactate and Actinobacteria, and (3) Actinobacteria, Archaea, Fibrobacteres, and A:P. Genome wide associations with the metabolome and microbiome were present despite a small population size, suggesting markers for ruminal acidosis susceptibility exist.