The gut flora, as an important organ, was illustrated to play a significant role in human health. Deciphering the gut flora diversity and their function is the recent crucial work. The next-generation sequencing arise the best chance to improve our knowledge on our gut flora. In 2010, we first built the gene catalog of human intestinal gut flora, including 3.3M genes. With the enlargement of donor cohort, an updated gene catalog was figured out, which contains nearly 10M genes, including almost the complete gene of human intestinal flora. Meanwhile, our team developed a protocol for a metagenome-wide association study (MGWAS) and established a new strategy-metagenomic linkage group (MLG) to find the role of "dark matter" bacterial. Based on these database and algorithm, hundreds of biomarkers in gut flora on T2D and other metabolic diseases were discovered, the further mechanism studies on model animals are important to validate their in vivo function. With the ever-increasing progress, the personalized health, nutrition and therapeutic intervention will more rely on the usage of human intestinal gut flora information.