Abstract
Healthy dietary patterns are associated with long-term health, but diet-quality scores do not reveal how habitual dietary information is represented in human biological phenotypes. Here we linked habitual dietary assessment with preceding health records and contemporaneous clinical chemistry, serum metabolomics and serum Raman spectra in community-dwelling Japanese adults. Higher diet quality corresponded to a more favorable preceding health profile, but did not define discrete states across contemporary multivariate phenotypes. Instead, specific dietary information was recoverable across these layers: Raman spectra provided predictive information complementary to clinical and metabolomic measurements for multiple dietary variables. Raman variation corresponding to β-carotene equivalent could be traced to carotenoid-assigned bands and aligned with a broader plant-food-related dietary dimension. These findings show that habitual diet is represented not as a single biological state but through biologically traceable dietary dimensions distributed across complementary phenotypic layers.