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First published 20 July 2015

Simulating the Influence of Diet on the Intestinal Microbiome Composition

Mark Read, Andrew J. Holmes, Madison Hartill-Law, Samantha Solon-Biet, David Raubenheimer, and Stephen J. Simpson

Abstract (Excerpt)

Diet is a driving factor in the emergence of western lifestyle disease, and of the gut microbe community (micro-biota) composition, which in turn has been linked to a host of diseases. There are many dimensions comprising ‘diet’: macronutrient distribution, the proportion of protein, carbohydrate and fat in food; energy density, the ratio of calories to food weight; intake pattern, the times at which we eat, and our incorporation of periods of fasting; and macronutrient source, such as carbohydrates in the form of sugar, complex carbohydrates or fibre. The rational design of diet interventions requires the integration of all these dimensions, which is challenging to do experimentally.

We are developing a simulation that integrates these diet dimensions to investigate how diet drives microbiota community composition. The simulation is agent-based, and explicitly represents individual bacteria cells and their location in the gut.