Taking a metagenomic view of human nutrition

Purpose of review Humans harbor microbial communities throughout the gastrointestinal tract that both respond to and modify orally ingested macronutrients, bioactive compounds, and xenobiotics; for example, the metabolism of polyphenols, heterocyclic amines, and phosphatidylcholine. However, the composition and physiological impact of our diet is also linked to the methods of food production, preparation, and consumption, which are altered by environmental and food-borne microbial communities. Metagenomic analyses spanning these various steps in human nutrition will be critical for a more comprehensive view. Recent findings Studies in humans and animal models have highlighted the key role that diet plays in shaping gut microbial ecology, and how the trillions of microbes in the gut (microbiota) enable the digestion of substrates inaccessible to our own human enzymes. These transformations have been implicated in a variety of diseases and disorders, ranging from obesity, inflammatory bowel disease, heart disease, to cancer. Summary In order to move towards personalized nutrition and medicine, it is important to take into account both our host and microbial genomes. The resulting metagenomic view of human nutrition, ranging from the initial biotransformations of food to digestion and the end result on human physiology, could have wide-ranging implications for food science, human evolutionary biology, and microbial ecology.