One of the most significant discoveries in life sciences and medicine in recent years is that we humans are symbionts with a large number of microbes. These microbes reside on all over our surface, with the major portion of the population being in the digestive tract. The gut microbiota (microbial community) consists of up to 1,000 species of bacteria and its number exceeds ten-times of that of the human cells. Throughout the history of co-evolution, humans and microbes have become dependent on each other, and as the result developed a complex web of specific interactions. Recent development of the fast and cost-effective next generation sequencing (NGS) technology enabled the researchers to dissect the structure and function of the gut microbiota and their associations with human physiology in much detail. This newly-blooming field of human-microbial genomics will completely change the way we see and treat ourselves.