The Department of Microbial Pathway Engineering was originally separated from the Department of Microbial Fermentation and Bioengineering and became an independent department in 1998. In the earlier years, the department focused on improving the production of antibiotics from soil microorganism through fermentation process optimization. In 1986, Key Laboratory of Biotechnology of Antibiotics, National Health and Family Planning Commission, was founded. As one of the most important parts affiliated to the key laboratory, the department started the studies of genetics and molecular biology of streptomyces to develop new antibiotics. In close collaboration with sister departments, like department of China Pharmaceutical Culture Collection and Department of Microbial Chemistry, the department successfully developed many clinically used antibiotics first in China, such as griseofulvin, midecamycin, spiramycin, kanamycin, trichomycin, ribostamycin and rapamycin (sirolimus). The department also invented the technology of teicoplanin production and the patent was transferred to a pharmaceutical company in South Korea. Moreover, Prof. Wang Yiguang and her colleagues employed modern microbial technology and invented the Category I new drug carrimycin, approved in 2019 by National Medical Products Administration, and clinical investigations have demonstrated carrimycin is a safe anti-infective drug with excellent therapeutic effect. The patents of carrimycin have been transferred to Shenyang Tonglian Group Co., Ltd. and its success, as a superior example, contributes a lot for the development or upgrade of microbial drugs and antibiotics.

The department currently focuses on development and innovation of microbial drugs, and receives funding from National Natural Science Foundation of China, National Significant New Drugs Creation, National Key Research and Development Program of China, Innovation Project in Chinese Academy of Medical Sciences, etc. In addition, the department continues collaborating with companies to finish important projects in the area of microbial drugs. The research interests of the department include: (1) Innovation of microbial genome mining and antibiotic-producer screening; (2) Biosynthetic studies of microbial secondary metabolites; (3) New antibiotic discovery driven by bioengineering and combinatorial biosynthesis, and rational design to increase the antibiotic production yield and simplify the production process; and (4) Characterization of unusual enzymes from microorganism and in vitro enzymatic synthesis of pharmaceutical intermediates.

Prof. Wang Yiguang served as the first head of the department since 1998. Prof. Che Yongsheng became the head in 2019 and Prof. Wu LinZhuan serves as the vice head now. There are 16 research scientists in the whole department, including five professors, one associate professor, nine assistant professors and one senior technician. Five professors, Che Yongsheng, Wu Linzhuan, Yang Zhaoyong, He Weiqing and He Haiyan, all established their independent laboratories.