Increased Resolution of Food Intake and Gut Microbiome in Precision Dietary Therap

High-resolution --omic phenotyping tools are allowing precision dietary therapies to gain tractability by providing molecular views of the impacts of diet on health. In the process, we are learning that interactions of ingested food and gut microbes are intimately-linked with health. This is challenging clinicians and scientists to consider gut microbes as they deliver precision dietary therapy that 1) achieves the goal of disease amelioration and 2) meets an individual's nutrient requirements. This dissertation discusses the development and application of two new high-throughput phenotyping approaches, foodomics and gut microbiome biogeography. Gut microbiome biogeography provides deeper resolution of gut microbes in the form of a bacterial microbiome map of the gut. Foodomics provides deeper resolution of food intake by providing molecular-level data on ingested nutrients in brand-name foods consumed by the public. Together, these tools allow for precise and detailed documentation of nutrients and gut microbes when a person or animal is administered precision dietary therapy. These tools allow researchers to manipulate nutrients in diet, monitor microbiome responses, interrelate the data with clinical phenotype, and pave the way to improved care of patients receiving precision dietary therapy.