Raw materials and manufacturing environment as determinants of miso microbial community

Miso is a Japanese traditional fermented food with soybeans, salt and kōji, 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 miso products from Gomi-shoyu (Yamanashi, Japan) at three distinct fermentation stages: initial (day one), intermediate (four months), and advanced (ten months). All samples, except the ten-month miso, were fermented in wooden barrels. We collected samples from the manufacturing facility, extracted DNA, and performed high-throughput 16S rRNA sequencing to generate amplicon sequence variants (ASVs). Our analysis revealed that the genus Staphylococcus dominated across all miso samples, with Macrococcus and Enterococcus also showing significant presence, particularly in the four-month miso. Notably, Staphylococcus sequences in the miso matched those found in rice and barley koji, indicating the influence of raw ingredients on the initial microbial community. Additionally, the wooden barrels exhibited a microbial profile similar to the miso, suggesting their role in maintaining consistent fermentation conditions. These findings underscore the critical importance of both raw ingredients and manufacturing equipment in shaping the microbial composition and evolution of miso throughout the fermentation process.