Research Progress in Multi-Omics Analysis of Dairy Products: Nutritional Quality, Safety Evaluation, and Health Functions

This review evaluates multi-omics applications in dairy research across nutrition, safety, and health. Through multi-omics integration, we reveal nutrient differences driven by species, rearing practices, and processing techniques, identify protein patterns and allergen profiles, and construct adulteration detection fingerprints and species-specific peptide markers, thereby improving the timeliness and accuracy of safety assessment. The coupling of metagenomics and metabolomics effectively predicts spoilage-related microbial risks, enabling better risk control. Furthermore, multi-omics approaches systematically elucidate the functional mechanisms of bioactive peptides (e.g., ACE-inhibitory peptides), clarify the prebiotic effects of functional oligosaccharides, and build interaction networks between dairy components and gut microbiota. The introduction of machine learning enables origin and shelf-life prediction, as well as the discovery of novel biomarkers, promoting personalized nutrition and precision fermentation strategies. However, the field is currently constrained by severe reproducibility issues arising from the absence of standardized operating procedures, excessive optimism regarding machine learning models that rarely generalize across laboratories or product matrices, and a persistent disconnect between laboratory-scale biomarker discovery and industrial implementation. Without rigorous cross-platform validation and openly shared multi-omics reference datasets, most published markers remain unfit for regulatory or industrial application. Future efforts should establish standardized workflows and expand the evidence base to drive the dairy industry toward safer, healthier, and more traceable directions.