The human microbiome is an emerging research area of interest with a series of reports on associations with various diseases and health, mainly due to advances in comprehensive analysis with the advent of next-generation sequencers. Fecal microbiota transplantation, a powerful method for modulating gut microbiota, has been reported to be surprisingly effective for certain disease populations that cannot be treated with conventional drugs. These results provide the possibility of microbiome modulation as a new approach for drug discovery. In the United States, the Human Microbiome Project was initiated in 2010 and many human microbiome data have been acquired, archived, and published. This has led to the emergence of a number of biopharmaceutical companies with clinical stage pipelines. Some of the most advanced pipelines are in the late clinical stage. However, issues such as the variability of data generated by different assays/protocols and the lack of data from healthy individuals as a reliable reference dataset should be addressed to further facilitate microbiome research and drug discovery based on human microbiome research. In Japan, in particular, established pharmaceutical companies tend to be reluctant to use these new approaches, as seen in human genome-based drug discovery. This may result in increased barriers to entry into emerging markets and a potential loss of opportunity. Since human microbiome research, especially gut microbiome research, has long been addressed by various research groups in Japan, microbe expertise and technology is high mainly in academia. It is important for Japanese industry to utilize the existing expertise of academic research groups. To accelerate the industrial use, Japan Microbiome Consortium (JMBC) was established in 2017, and its member companies include 33 pharmaceutical, chemical, food, and testing companies in Japan, including major companies and bio-venture companies. In this lecture, I will introduce the background of the establishment of JMBC and share the activities of the project for establishment of the measurement infrastructure and the project for construction of the database of healthy persons, which have been common goals. I would like to summarize the recent global trends and activities on drug discovery based on the human microbiome, as well as issues for obtaining approval and launching the drug. We would also like to discuss how we can activate drug discovery activities as one of JMBC's activities and lead to the creation of innovative new drugs.