Foodomics for personalized nutrition: how far are we?

• Personalized nutrition can maintain an individual within his optimal metabolic space.
• Foodomics are crucial tools to determine an individual's optimal metabolic space.
• Gut microbiota must be considered to measure metagenome–hyperbolome–diet interplay.
• Lack of consistent, rigorous data integration tools is the major challenge to be faced.

To effectively prevent the onset and reduce mortality from non-communicable diseases, we must consider every individual as metabolically unique to allow for a personalized management to take place. Diet and gut microbiota are major components of the exposome that interact together with a genetic make-up in a complex interplay to result in an individual's metabolic phenotype. In this context, foodomics approaches (such as nutrigenetics, nutrimetabolomics, nutritranscriptomics, nutriproteomics and metagenomics) are essential tools to assess an individual's optimal metabolic space. These have recently been applied to large human cohorts to identify specific gene-metabolite, diet-metabolite and gene–diet interactions. As the gut microbiota is a key player in metabolic homeostasis, we suggest following a holistic investigation of metagenome–hyperbolome–diet interactions, the findings of which will provide the basis for developing personalized nutrition and personalized functional foods. However, examining these three-way interactions will only be possible when the challenge of large datasets integration will be overcome.