Abstract:As the new scientific field of studying the gene function and interactions of microbial community, metagenomics has largely contributed to the development and utilization of microbial resources, and made breakthrough progress in various fields, such as soil, oceans, human medical, pharmaceutical and so on. Metagenomics provided a novel approach for the discovery of new bioactive substances. Here we discuss some recent progress with emphasis on the opportunities and challenges in metagenomics applications.