The Microbe Division in RIKEN-BRC has been collecting, preserving, and distributing cultured microbial strains as one of the leading culture collections in the world since established as Japan Collection of Microorganisms (JCM) in 1981. JCM aims to contribute to scientific communities by maintaining and serving high-quality microbial resources useful for general microbial studies and various research fields particularly in health and environmental science. JCM has participated in the National BioResource Project supported by the Ministry of Education, Culture, Sports, Science and Technology of Japan as the core facility for "General Microbes".

JCM maintains approximately 20,700 strains as of Apr. 2012, and the approximate numbers of the available strains from JCM are: 8,300 strains of aerobic and anaerobic bacteria including actinomycetes, 370 strains of archaea, and 4,800 strains of fungi including yeasts (in total ca. 13,500 strains). Strains held at JCM are limited to those classified in Risk Group 1 or 2. Information of the available strains is opened to the public through the JCM On-line Catalogue Database. Genomic DNA samples of some strains are also distributed in cooperation with RIKEN BRC-DNA Bank. More than 3,500 strains are annually distributed to domestic and overseas researchers.

JCM is working to continuously improve the functions as a microbial resource center, to exploit new microbial resources, to describe novel microbial taxa, and to develop the methods for investigating and handling extremophiles, yet-uncultured microorganisms, and microbial communities. JCM has been acquired the certification of ISO 9001 : 2008 for its quality management system to maintain and improve the quality of its service. In order to promote the use of the microbial strains, JCM regularly issues mailnews and newsletter (in Japanese), and gives training courses for basic and advanced microbial techniques.

JCM welcomes a deposit of microbial strains published or designed to be published in scientific papers as well as an order for microbial cultures.