Natto beans are whole soybeans that have been fermented with a specific bacterium called Bacillus subtilis, producing a sticky, pungent food that’s been a staple in Japan for centuries. Unlike other soy products, natto is fermented without salt and retains the whole bean shape, resulting in a unique nutritional profile packed with vitamin K2, protein, and a clot-dissolving enzyme found in no other common food.
How Natto Is Made
The process starts with soaking dried soybeans, then boiling or steaming them until soft. The cooked beans are mixed with Bacillus subtilis bacteria and left to ferment at around 40°C (104°F) for 12 to 24 hours. During that time, the bacteria break down proteins in the soybeans, creating natto’s signature sticky threads and sharp flavor. A shorter ferment produces a milder taste, while a full 24 hours intensifies the flavor considerably.
Traditionally, the bacteria came from rice straw. Bacillus subtilis naturally lives on straw surfaces and, because it forms hardy spores, survives the boiling process. Today, most producers use a pure starter culture for consistency. Natto is one of the few fermented foods where bacteria, rather than yeast or mold, drive the entire fermentation.
What Natto Tastes and Feels Like
Natto is an acquired taste, even in Japan. The flavor is bitter, salty, and earthy, with a strong pungent smell that catches people off guard. The texture is what makes it truly distinctive: stirring the beans creates a gooey, almost creamy consistency with long sticky strings stretching off your chopsticks. This sliminess, called “neba neba” in Japanese, is a hallmark of the food and something many people either love or can’t get past.
The traditional way to eat natto is over hot rice for breakfast, often mixed with soy sauce and mustard. It also shows up as a topping on rice bowls alongside seaweed, okra, and sometimes raw egg. Stirring the beans vigorously before eating, sometimes 50 times or more, is considered the proper technique to develop the sticky threads and mellow the flavor slightly.
Vitamin K2 and Bone Health
Natto is one of the richest dietary sources of vitamin K2, specifically a form called MK-7. During fermentation, Bacillus subtilis synthesizes this vitamin in large quantities. Vitamin K2 plays a direct role in calcium metabolism: it activates proteins that help deposit calcium into bones and teeth while keeping it out of arteries and soft tissue. This is different from vitamin K1 (found in leafy greens), which primarily supports blood clotting.
A randomized, placebo-controlled trial in healthy postmenopausal Japanese women found that Bacillus subtilis supplementation significantly reduced markers of bone breakdown after 12 weeks. The women taking it also showed increased levels of beneficial Bifidobacterium in their gut and decreased levels of harmful Fusobacterium bacteria, suggesting the fermentation bacteria themselves act as a probiotic. The researchers concluded that the combination of improved gut bacteria and reduced bone resorption contributed to better bone mineral density.
Nattokinase and Heart Health
The enzyme nattokinase forms during fermentation and is unique to natto. It works as a natural clot-buster, directly breaking down fibrin, the protein mesh that holds blood clots together. It also stimulates your body’s own clot-dissolving system by increasing tissue plasminogen activator, essentially helping your blood maintain healthy flow through two separate pathways.
Beyond its clot-dissolving ability, nattokinase has been linked to lower blood pressure and reduced buildup of arterial plaque. These effects make natto a food of particular interest for cardiovascular health, though people taking blood-thinning medications like warfarin need to be cautious. Natto’s extremely high vitamin K content can interfere with how those drugs work, and medical guidelines classify soy products as vitamin K foods that need to be consumed consistently rather than sporadically if you’re on anticoagulants.
How Natto Compares to Other Fermented Soy
Tempeh, miso, and natto all start with soybeans, but the fermentation organisms and end results differ significantly. Tempeh uses a mold that binds the beans into a firm cake, producing a mild, nutty flavor. Miso is fermented with a combination of mold and salt into a thick paste used mainly as a seasoning. Natto’s bacterial fermentation is what sets it apart nutritionally.
The biggest differences come down to two compounds. Nattokinase is exclusive to natto. Tempeh and miso don’t contain it. Vitamin K2 levels in natto far exceed what you’ll find in other fermented soy foods. Miso lacks meaningful K2 content, and tempeh contains only trace amounts compared to natto. All three are good protein sources, and tempeh matches natto in fiber content, but for the specific cardiovascular and bone-related nutrients, natto stands alone.
Making Natto at Home
Homemade natto requires just two ingredients: soybeans and a Bacillus subtilis starter culture, which is available online as a powder. Soak the beans overnight, then steam or pressure cook them until they’re soft enough to crush easily between your fingers. Mix in the starter culture while the beans are still warm, spread them in a thin layer in shallow containers, and cover loosely to allow airflow.
Temperature control is the critical step. The beans need to stay between 37 and 45°C (99 to 113°F) for the entire fermentation period. An oven with just the light on, a food dehydrator, or a yogurt maker can work. Fermentation takes 12 to 24 hours, and you’ll know it’s working when white, sticky threads appear between the beans. After fermentation, refrigerate the natto for at least a few hours before eating. This rest period mellows the flavor and firms up the texture. Homemade natto keeps in the fridge for about a week or can be frozen for several months.