The extent of metabolic interactions between symbiotic intestinal microbes and the human host, and their system-wide effects on the host physiology are beginning to be understood. The metabolic capacity encoded by the intestinal microbiome significantly extends that of the host, making many of man's physiological characteristics an outcome of a human-microbe co-metabolism. A detailed characterization of the composition and function of the gut microbial ecosystem is required to foster the understanding of its mechanisms and impact. The most recent research on the intestinal ecosystem is reviewed here, with specific attention to the ecological aspects including the anticipated effects of probiotics and prebiotics. Finally, the post-genomics approaches that advance discovering the functionality of intestinal bacteria are addressed.