Nutritional research has emerged in the last century from the study of nutrients as a means of nourishment to the general population to the quest for wellness improvement through specific food components. Advances in nutrigenomics technologies have allowed nutrition scientists to be for the first time at the forefront of nutritional research. Such advances have given them the ability to discern new vital scientific discoveries specifically for the development of new tailored dietary patterns. In this, nutritional metabonomics has rapidly evolved into a very powerful bioanalytical tool able to assess multi-parametric metabolic responses of living organisms to specific dietary interventions. Nutritional metabonomics therefore provides a systematic approach through the comprehensive analysis of metabolites aiming today at the quest for homeostatic balance which is dependent not only on the host but also on the crucial metabolic interactions with microbial symbionts.