Japanese Natto Fermentation Science and Bacillus subtilis var natto Cultures

Japan — natto tradition from at least the early Heian period (10th century); wara (rice straw) natural fermentation method predates commercial culture production; Mito City (Ibaraki) is the historical capital of natto culture

While natto's cultural role in Japanese cuisine is broadly documented, its microbiology represents one of the most fascinating chapters in fermented food science. Natto is produced by inoculating cooked soybeans with Bacillus subtilis var natto—a specific strain of the ubiquitous soil bacterium, selected for its ability to produce nattokinase (an enzyme with documented fibrinolytic properties that has generated significant pharmaceutical research) and the characteristic poly-gamma-glutamic acid polymer that creates natto's defining sticky, thread-pulling mucilage. The fermentation occurs at precisely 40–42°C for 16–24 hours in shallow trays or straw containers—B. subtilis var natto is an aerobic bacterium requiring oxygen access, which is why natto is never made in sealed containers. The straw fermentation tradition (wara natto) allowed natural B. subtilis inoculation from rice straw's inherent bacterial flora—the bacteria lived on the straw surface and colonised the beans naturally during the fermentation period. Modern commercial natto uses laboratory-isolated B. subtilis var natto strains in specific concentrations for consistent results, but the underlying biochemistry is identical to the straw tradition: the bacteria produce amylase, protease, and lipase enzymes that partially digest the soybean's protein and fat, creating the characteristic amino-acid-rich flavour compounds and the nattokinase polymer. Regional natto varieties—from Mito (Ibaraki's natto capital), Kyoto, and Hokkaido—use different soybean varieties, fermentation times, and post-fermentation maturation to produce distinct flavour profiles.

Pungent, ammonia-adjacent, deeply umami-savoury with bitter notes; mustard and soy sauce condiments bridge the flavour gap for less experienced palates; the mucilaginous polymer creates a unique texture that many Japanese consider as pleasurable as the flavour is challenging