Interaction between the Microbiome and Diet: The Hologenome Concept

Abstract

All plants and animals, including humans, are holobionts consisting of a host and diverse microorganisms, referred to as the microbiome or microbiota. The hologenome concept posits that the holobiont with its hologenome (sum of host and microbiome genes) can function as a single entity, acting in consortium, and therefore also as a unit of selection in evolution. Diet affects the microbiome by increasing or decreasing the population of some bacteria relative to others and by introducing new bacteria into the microbiome. Such phenomena can result in physiological changes within the host as well as within the holobiont as a whole. Novel microbes can be introduced into the microbiome by uncooked food; Changes in the relative number of bacteria can occur in the colon where food remnants, such as dietary fiber, that escape digestion in the upper digestive tract, are broken down into short chain fatty acids and many other compounds-beneficial, neutral or harmful. Diet-induced changes in the microbiome contribute to the health of humans by providing nutrients, priming the immune system, regulating development and eating behavior, and contributing to energy homeostasis, obesity and occasionally to disease.