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A growing body of research on nutrition omics has led to recent advances in cardiovascular disease epidemiology and prevention. Within the PREDIMED trial, significant associations between diet-related metabolites and cardiovascular disease were identified, which were subsequently replicated in independent cohorts. Some notable metabolites identified include plasma levels of ceramides, acyl-carnitines, branched-chain amino acids, tryptophan, urea cycle pathways, and the lipidome. These metabolites and their associated pathways have been associated with incidence of both cardiovascular disease and type 2 diabetes. Future directions in precision nutrition research include: a) developing more robust multimetabolomic scores to predict long-term risk of cardiovascular disease and mortality; b) incorporating more diverse populations and a broader range of dietary patterns; and c) conducting more translational research to bridge the gap between precision nutrition studies and clinical applications.