Most Japanese fermented foods are defined by Aspergillus oryzae — the koji mold that drives miso, shoyu, sake, and shio koji. Natto is the exception. Its fermentation organism is a bacterium, its texture is unlike any other fermented food in the Japanese pantry, and its bioactive compound profile — nattokinase, vitamin K2, polyglutamic acid — makes it one of the most scientifically interesting foods in the world. It also smells like a strong argument against ever eating it. Both things are true.

What Natto Is

Natto (納豆) is whole soybeans fermented with Bacillus subtilis var. natto — a spore-forming bacterium selected over centuries for its ability to ferment soybeans at warm temperatures while producing the characteristic sticky, stringy texture and pungent aroma that define the product. It has been consumed in Japan for at least 1,000 years, with historical records suggesting its origins in the Kanto region, where it remains most popular today.

Unlike miso or shoyu, which require weeks to years of fermentation, natto is produced in approximately 24 hours at 40–42°C — one of the fastest fermentation processes in traditional Japanese food production. The speed is a function of B. subtilis‘s rapid growth rate under warm, humid conditions and the relatively simple biochemical transformation required: the soybeans are already cooked and protein-accessible; the bacterium simply needs to grow across the surface and begin its enzymatic activity.

The Fermentation Organism: Why Bacillus subtilis Is Different

Bacillus subtilis is a fundamentally different type of microorganism from the molds and yeasts that drive most Japanese fermentation. Several properties distinguish it:

Spore Formation

B. subtilis forms highly resistant endospores under adverse conditions — structures that can survive boiling, desiccation, UV radiation, and extreme pH. This spore-forming ability has two practical consequences for natto. First, natto’s fermentation organism is far more robust than the koji mold or sake yeast: spores survive transit through the stomach’s acidic environment and germinate in the intestinal environment, giving natto genuine and well-documented probiotic activity that most other fermented foods cannot match. Second, natto starter cultures are stable at room temperature for months, making them easy to handle compared to live mold cultures.

Alkaline Fermentation

Unlike lactic acid fermentation (which produces acids and drops pH) or alcoholic fermentation (which produces ethanol), B. subtilis fermentation is alkaline. The bacterium produces ammonia as a byproduct of protein breakdown, raising the pH of the fermenting soybeans from approximately 6.5 to 7.5–8.0. This alkalinity is responsible for much of natto’s distinctive pungent aroma — ammonia and the volatile amines produced alongside it are the primary contributors to the smell that divides opinion so dramatically.

Polyglutamic Acid: The Source of the Strings

The sticky, stringy texture of natto — the neba-neba (粘々) quality that surprises first-time eaters — is produced by polyglutamic acid (PGA), a polymer of glutamic acid secreted by B. subtilis as a protective capsule material. PGA is water-soluble and forms long, elastic strings when stretched — producing the characteristic threads that appear when natto is stirred or lifted with chopsticks.

PGA is not merely a textural curiosity. It has several biologically active properties: it is a prebiotic substrate for certain gut bacteria, it has demonstrated moisture-retention properties relevant to both gut and skin health research, and it represents one of the few natural food sources of high-molecular-weight polyglutamic acid. The strings are, in biochemical terms, a functional biomaterial produced by the bacterium for its own protective purposes and co-opted by the food system for entirely different reasons.

Nattokinase: The Enzyme That Generated the Most Research Interest

Nattokinase is a serine protease enzyme produced by B. subtilis var. natto during fermentation. It was first isolated in 1987 by Dr. Hiroyuki Sumi at the University of Chicago, who identified its fibrinolytic activity — its ability to degrade fibrin, the protein that forms blood clots.

The Biochemical Mechanism

Nattokinase degrades fibrin directly through proteolytic cleavage — it cleaves fibrin strands at specific peptide bonds, dissolving clot structure. It also appears to activate the body’s own fibrinolytic system by enhancing the production of tissue plasminogen activator (t-PA) and inhibiting plasminogen activator inhibitor-1 (PAI-1). This dual mechanism — direct fibrinolysis plus endogenous fibrinolytic system activation — distinguishes nattokinase from simpler fibrinolytic agents.

What the Evidence Shows

The evidence base for nattokinase’s effects in humans is more substantial than for most dietary enzyme claims, but still limited in scale and duration.

In vitro and animal studies consistently demonstrate fibrinolytic activity at physiologically relevant concentrations. These findings are mechanistically sound and reproducible.

Human clinical trials — of which several small-scale studies have been published — have shown modest reductions in blood viscosity, fibrinogen levels, and factor VIII activity in human subjects consuming nattokinase supplements or natto. A 2009 randomised controlled trial in Scientific Reports found statistically significant reductions in thrombus formation in participants consuming nattokinase over 26 weeks. Effect sizes are modest and study populations small.

The oral bioavailability question remains partially open. Stomach acid and digestive proteases degrade proteins, and whether sufficient intact nattokinase reaches the circulation after oral consumption to produce systemic effects is debated. Some evidence suggests that B. subtilis spores in natto may produce nattokinase in the gut after germination, partially bypassing the oral degradation issue.

Vitamin K2 (MK-7): The Better-Evidenced Bioactive

If nattokinase represents natto’s most intriguing but uncertain bioactive, vitamin K2 in the form of menaquinone-7 (MK-7) represents its most clearly evidenced nutritional contribution.

Natto is by far the richest dietary source of MK-7 — a form of vitamin K2 with a long biological half-life (approximately 72 hours, compared to MK-4’s 4–6 hours) that produces more sustained and bioavailable vitamin K activity than shorter-chain menaquinones. A single 100g serving of natto contains approximately 870–1,000 μg of MK-7 — far exceeding the adequate intake recommendations and orders of magnitude more than any other commonly consumed food.

What MK-7 Does

Vitamin K2 activates matrix Gla protein (MGP) and osteocalcin — proteins that direct calcium to bone tissue rather than arterial walls. Inadequate vitamin K2 activity is associated with arterial calcification and reduced bone mineralisation. MK-7 supplementation has been shown in prospective studies and randomised trials to reduce arterial stiffness markers and improve bone mineral density in postmenopausal women. The evidence base for MK-7’s cardiovascular and bone health effects is among the stronger in the fermented food literature — more robust than nattokinase evidence by a significant margin.

Nutrition Beyond the Headlines

Natto’s nutritional profile extends beyond its headline bioactives.

The Probiotic Distinction

Among Japanese fermented foods, natto has the most robust probiotic credentials — for a specific biochemical reason. B. subtilis spores survive gastric acid and bile salts that would kill most lactobacilli. Studies tracking B. subtilis in the gut after natto consumption have confirmed that viable spores germinate in the intestinal environment, producing a transient but genuine increase in B. subtilis populations and associated metabolic activity.

This distinguishes natto from miso and other fermented foods whose live culture benefits depend on surviving the highly acidic gastric environment — a challenge that most LAB species manage poorly under realistic conditions. The spore survival mechanism gives natto’s probiotic activity a mechanistic advantage that is not shared by most other fermented foods.

Japanese Fermented Foods and the Gut Microbiome: What the Science Actually Shows

How Natto Is Produced

The production process is straightforward relative to most Japanese fermented foods. Soybeans are soaked, steamed, inoculated with B. subtilis var. natto spores (commercially available as starter cultures), portioned into small containers, and incubated at 40–42°C for 18–24 hours. The warm incubation temperature is critical — it is optimal for B. subtilis growth while inhibiting most potential spoilage organisms. After fermentation, natto is refrigerated for at least 24 hours before consumption; this post-fermentation rest period allows the flavour and texture to develop further and the ammonia aroma to mellow slightly.

Home production is genuinely accessible — simpler than miso and requiring no specialized equipment beyond a warm incubation environment (an oven with the light on, a yogurt maker, or a temperature-controlled fermenter all work). The main variables are inoculation rate (typically 0.1–0.2g starter per kg soybeans) and incubation temperature consistency.

Eating Natto: A Note on Palatability

The polarising reputation of natto is real and has a biochemical basis — the ammonia and volatile fatty acid content of a well-fermented natto is genuinely assertive. For those approaching natto for the first time, several practical points are worth knowing.

First, younger natto — 1–2 days post-fermentation — has a milder aroma than older natto, because ammonia production continues slowly during refrigerated storage. Consuming natto close to its production date produces a less challenging introduction than an older package.

Second, mixing natto vigorously before eating — the traditional practice of stirring 40–50 times — develops the PGA strings and distributes the fermentation byproducts more evenly, which many people find improves both texture and palatability.

Third, the traditional condiments — soy sauce and Japanese mustard (karashi) — are not arbitrary flavour additions. The glutamate in soy sauce adds umami that the natto’s own flavour profile somewhat lacks (its alkaline fermentation produces little free glutamate compared to miso or shoyu), and the mustard’s sharpness cuts through the fatty richness of the soybeans. The combination is nutritionally and biochemically complementary as well as traditional.