Ito, K.; Yamaguchi, M.

We identified the microbiota of miso products of Gomi-shoyu (Yamanashi, Japan) at different fermentation stages (first day, four months, and ten months). All samples were fermented in wooden barrels, except for the ten-month miso. Sample collection from the manufacturing facility was followed by DNA extraction and high-throughput 16S rRNA sequencing, with the resulting amplicon sequence variants (ASVs). The genus Staphylococcus dominated all miso samples, while Macrococcus and Enterococcus were also prevalent, especially in the four-month miso. The Staphylococcus sequences from rice and barley koji matched those found in the miso, implying how raw ingredients shape the initial microbial population. Furthermore, wooden barrels exhibited a microbial profile similar to miso, suggesting its role in promoting consistent fermentation. Thus, our findings suggest that the raw ingredients and manufacturing equipment both play a critical role in shaping the microbial composition of miso during fermentation.