The Extended Nutrigenomics - Understanding the Interplay between the Genomes of Food, Gut Microbes, and Human Host

Abstract

Comprehensive investigation of nutritional health effects at the molecular level requires the understanding of the interplay between three genomes, the food, the gut microbial, and the human host genome. Food genomes are researched for discovery and exploitation of macro- and micronutrients as well as specific bioactives, with those genes coding for bioactive proteins and peptides being of central interest. The human gut microbiota encompasses a complex ecosystem in the intestine with profound impact on host metabolism. It is being studied at genomic and, more recently, also at proteomic and metabonomic level. Humans are being characterized at the level of genetic pre-disposition and inter-individual variability in terms of (i) response to nutritional interventions and direction of health trajectories; (ii) epigenetic, metabolic programming at certain life stages with health consequences later in life and even for subsequent generations; and (iii) acute genomic expression as a holistic response to diet, monitored at gene transcript, protein and metabolite level. Modern nutrition science explores health-related aspects of bioactive food components, thereby promoting health, preventing, or delaying the onset of disease, optimizing performance and assessing benefits and risks in individuals and subpopulations. Personalized nutrition means adapting food to individual needs, depending on the human host's life stage, -style, and -situation. Traditionally, nutrigenomics and nutri(epi)genetics are seen as the key sciences to understand human variability in preferences and requirements for diet as well as responses to nutrition. This article puts the three nutrition and health-relevant genomes into perspective, namely the food, the gut microbial and the human host's genome, and calls for an "extended nutrigenomics" approach in order to build the future tools for personalized nutrition, health maintenance, and disease prevention. We discuss examples of these genomes, proteomes, transcriptomes, and metabolomes under the definition of genomics as the overarching term covering essentially all Omics rather than the sole study of DNA and RNA.

Keywords: bioactive; biomarker; epigenetics; gut microbiota; nutrigenetics; nutrigenomics; personalized nutrition.

Figure 1

Extended nutrigenomics for nutrition and health: the plant genome for example affects the human genome either through direct impact of its bioactives (incl. proteins and peptides), or indirectly via the gut microbial metabolism providing nutrients on which specific gut bacteria can feed.

Figure 2

Functions of plant-derived bioactive peptides released by enzymatic digestion or fermentation: again, the example of the plant world is chosen with soy, rice, cereals, and sunflower as sources. Through enzymatic digestion or fermentation, bioactive peptides can be released either in vitro (by processing) or in situ in vivo (upon digestion) that can exert various beneficial effects ranging from protection against excessive oxidative stress and even cancer; via cardiovascular to immune benefits.

Figure 3

Workflow of bioinformatics-driven discovery of bioactive peptides. Blue: bioinformatics; green: peptidomics; orange: in vitro; purple: in vivo.

Figure 4

Food compounds (macro- and micronutrients) are digested and absorbed the gastro-intestinal tract (GIT) before they may reach various other body tissues. In the GIT, food stuffs interact with and are partly metabolized by an enormous quantity and diversity of bacteria residing in the stomach and, in particular, in the gut.