Bacillus subtilis var. natto is a strain of the Hay Bacteria (Bacillus subtilis) in the family Bacillaceae that is specifically associated with the fermentation of soybeans to produce the traditional Japanese food natto. The genus name Bacillus derives from Latin meaning “small rod,” referring to the rod-shaped morphology of the bacteria, while subtilis means “fine” or “slender,” describing the organism’s delicate microscopic form. The varietal designation natto refers to the fermented soybean food in which this bacterial strain plays the central role. This bacterium has been domesticated through repeated use in fermentation and is adapted to thrive in the warm, nutrient-rich conditions present during natto production.

Bacillus subtilis var. natto is a Gram-positive, aerobic, spore-forming bacterium capable of surviving harsh environmental conditions through the formation of endospores. During fermentation, the bacterium grows on cooked soybeans and produces enzymes that break down soybean proteins and carbohydrates. This metabolic activity generates a variety of compounds that contribute to natto’s distinctive flavor, aroma, and sticky texture. One of the most notable characteristics of natto fermentation is the production of extracellular polyglutamic acid, which forms the characteristic viscous strands that appear when natto is stirred. Historically, natto fermentation likely originated in Japan through spontaneous fermentation of cooked soybeans by naturally occurring Bacillus subtilis strains present in rice straw, which traditionally served as a wrapping material for the beans. Over time, specific strains adapted for reliable fermentation were isolated and cultivated for controlled production. Today, commercial natto production typically uses purified starter cultures of Bacillus subtilis var. natto to ensure consistent flavor, texture, and microbial safety.

Bacillus subtilis var. natto is important because it transforms soybeans (Glycine max) into fermented natto. The fermentation process increases the digestibility of soybean proteins. The organism produces several notable metabolites during fermentation, including nattokinase, poly-γ-glutamic acid, and various peptides generated through protein breakdown. These compounds contribute both to natto’s distinctive sensory properties and to its nutritional profile. While Bacillus subtilis var. natto is generally considered a safe, probiotic, and industrial food-grade organism, rare, opportunistic infections, including bacteremia and meningitis, have been reported, particularly in immunocompromised individuals or those with severe comorbidities, often involving wild strains similar to common starter cultures.