Diet, environment and gut microbiota in the metagenomic era

The human gut microbiota is a complex consortium of trillions of microorganisms, whose collective genomes or “metagenome” contains at least 100-times as many genes as our own eukaryote genome (1). This essential “organ”, the microbiome, provides the host with enhanced metabolic capabilities, supplying energy, nutrients, bioactive compounds, provides an effective barrier or resistance to invading pathogens, resulting in education of the immune system, and modulation of gastrointestinal (GI) development. Furthermore this microbial community is also involved in detoxification of harmful exogenous and endogenous compounds. The role of the resident microbiota in the human gut and its profound effects on host health and daily well-being is now recognized as crucial. The composition of the intestinal microbiota plays a critical role in mammalian metabolism and, likely, in human health. Twins and mother-daughter pairs have more similar microbiota compositions than unrelated individuals, suggesting that there could be a genetic influence over the microbiota (2). However, monozygotic and dizygotic adult twins have equally similar microbiota, suggesting environment rather than genetics may drive familial similarities (2). The extent at which factors such as the environment and diet shape the human gut microbiota is still unclear, partly because these factors are often confounded. However, in terms of microbiota function, metabolic output and interactions with the host, diet and other exogenous factors like antibiotics or xenobiotic compounds also plays a dominant role.