Raw materials and manufacturing environment as determinants of miso bacterial community

Miso is a Japanese traditional fermented food with soybeans, salt and koji, and has gained attention among people for its sophisticated flavor and preservability. Koshu miso is a unique miso made by mixing two types of koji (rice and barley), and is produced primarily in Yamanashi Prefecture, Japan. We characterized the microbiota of Koshu miso at three distinct fermentation stages. Our analysis revealed that the genus Staphylococcus dominated across all miso samples. Notably, Staphylococcus sequences in the miso matched those found in rice and barley koji, indicating the influence of raw ingredients on the initial bacterial community. Additionally, analysis of the manufacturing environment suggested similarities between the environmental surfaces and miso, highlighting the importance of the manufacturing environment in serving as a medium for bacterial transfer. These findings underscore the critical importance of both raw ingredients and manufacturing equipment in shaping the bacterial composition and evolution of miso throughout the fermentation process.