The number of microorganisms inhabiting the human digestive tract exceeds the number of body cells by a factor of ten. This microbial community affects host physiology and host health. The metabolic potential of the gut microbiota is immense affording the extraction of energy from otherwise indigestible carbohydrates (dietary fiber) and the conversion of host-derived substances, non-nutritive dietary components and drugs. Recognized functions of the gut microbiota include provision of colonization resistance against pathogens and priming of both the innate and the acquired immune systems. However, the intestinal microbiota may also contribute to the development of diseases such as ulcerative colitis and colorectal cancer. Culture-dependent studies provided basic knowledge on the gut microbiota, but only the advent of culture-independent molecular methods led to a better understanding of host-microbe interactions. The application of metagenomics to the gut microbial ecosystem revealed truly remarkable correlations between certain diseases and the gut microbiome. It also led to the suggestion of the existence of a 'core microbiome' that encompasses key functions shared by each individual. However, the mechanisms underlying host-microbe interactions have not yet been unraveled.