Natto: The Sticky, Ancient Japanese Superfood of Vitamin K2, Nattokinase, and Gut-Friendly Bacillus subtilis

Natto is a traditional Japanese breakfast food made by fermenting whole soybeans with Bacillus subtilis var. natto for roughly 24 hours. The result is a sticky, pungent, strongly flavored dish that divides Western palates almost as sharply as it delivers nutritional value. Natto is arguably the single richest dietary source of vitamin K2 (menaquinone-7) in the human food supply, contains the fibrinolytic enzyme nattokinase, and provides a uniquely resilient probiotic organism — Bacillus subtilis — that survives stomach acid intact to colonize the gut.

This article covers the nutritional profile, evidence on cardiovascular and bone health, how to eat it, where to buy or make it, and the few people who should approach it cautiously.

History and Production
Vitamin K2 — The Cardiovascular and Bone Connection
Nattokinase — The Fibrinolytic Enzyme
Bacillus subtilis — A Different Kind of Probiotic
Broader Nutritional Profile
How to Eat It
Where to Buy or How to Make It
Who Should Be Cautious
Connections
Research Papers
Featured Videos

History and Production

Natto has been consumed in Japan for at least a thousand years, traditionally made by wrapping boiled soybeans in rice straw containing naturally occurring Bacillus subtilis and allowing them to ferment in a warm environment. Modern industrial production uses pure cultures in controlled temperature and humidity, producing a more consistent end-product. The signature sticky threads (ito-hiki) that stretch between the beans are polymers of poly-gamma-glutamic acid and fructans produced by the bacterium.

Vitamin K2 — The Cardiovascular and Bone Connection

Vitamin K comes in two major forms: K1 (phylloquinone) from leafy greens and K2 (menaquinone) primarily from fermented foods and animal products. Among the K2 menaquinones, the MK-7 subtype in natto has the longest half-life and most effectively activates vitamin-K-dependent proteins outside the liver — particularly osteocalcin (which directs calcium into bone) and matrix Gla protein (which keeps calcium out of arterial walls). The Rotterdam Study found that higher dietary K2 intake was associated with a 57% reduction in coronary heart disease mortality over 10 years. Observational epidemiology consistently correlates K2 intake with reduced arterial calcification and fewer hip fractures. Natto provides roughly 350–1000 µg of MK-7 per 100 g — an order of magnitude more than any other common food.

Nattokinase — The Fibrinolytic Enzyme

Nattokinase is a serine protease produced by Bacillus subtilis var. natto. In blood, it breaks down fibrin — the structural protein of clots — and mimics some effects of pharmaceutical fibrinolytics. Small human trials of nattokinase supplements (100–300 mg/day as FUs) have shown modest reductions in blood pressure, plasma fibrinogen, and platelet aggregation. Whether the amount consumed in a bowl of natto is bioavailable enough to produce these effects systemically is debated, and the nattokinase supplement literature far exceeds the literature on nattokinase from food.

Bacillus subtilis — A Different Kind of Probiotic

Unlike the Lactobacillus and Bifidobacterium species in most probiotic yogurts, Bacillus subtilis forms protective spores that survive stomach acid and emerge in the small intestine. It produces antimicrobial compounds that suppress pathogenic species, supports mucosal immunity, and may improve gut barrier integrity. It is one of the organisms in various commercial spore-based probiotic formulations.

Broader Nutritional Profile

A 100-gram serving (roughly one container) of natto provides approximately:

Calories: 210
Protein: 19 g — a complete plant protein
Fiber: 5 g
Vitamin K2 (MK-7): 350–1000 µg
Iron: 48% DV
Manganese: 70% DV
Copper, magnesium, phosphorus, zinc: significant amounts
Isoflavones (genistein, daidzein): richest among common soy foods

How to Eat It

Natto is traditionally served with rice, a small amount of soy sauce, Japanese mustard (karashi), and chopped green onions. Stirring vigorously before serving develops the sticky threads and mellows the flavor. Some Japanese eaters add a raw egg yolk or a beaten egg. For newcomers, mixing natto into fried rice, miso soup, or atop avocado toast can make the first attempts more approachable. The flavor is umami-forward with a hint of ammonia that fades as you acclimate.

Where to Buy or How to Make It

Commercial natto is sold frozen in roughly 50-gram single-serving styrofoam packets at Japanese and Korean grocery stores, and increasingly in well-stocked natural-food stores. It keeps in the freezer for months and thaws in about an hour. Home fermentation is straightforward: cook whole soybeans to a tender texture, add a small amount of commercial natto as a starter, and incubate at 40–42 °C for 24 hours in a covered container.

Who Should Be Cautious

Warfarin users. The high vitamin K content significantly interferes with warfarin anticoagulation. Maintaining consistent intake (not necessarily zero) is the standard recommendation — discuss with your anticoagulation clinic.
Soy allergy. Obviously contraindicated.
Active thyroid medication. Space soy foods several hours from levothyroxine dosing.
Low-histamine diet patients. Fermented foods including natto can be high in histamine.

Connections

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Featured Videos

Natto and Heart Health

What is Natto? Fermented Sticky Beans, K2 and Nattokinase

What Happens to People over 60 If They Eat Natto Every Day?

Recovery Foods after Fasting: Umenagashi & Natto

The Truth about Natto: Debunking the Myth of the Smelly Superfood

How I Use Nattokinase to Unclog Arteries

Nattokinase: Can You Take Too Much? Everything You Need To Know...

105: Can Nattokinase Improve Heart & Metabolic Health? with Dr. Ben Bikman

Nattokinase: Breakthrough Supplement For Heart Health?

Research Papers

The following curated PubMed topic searches lead to the peer-reviewed primary literature and systematic reviews that underpin the health claims discussed on this page. Each link opens PubMed in a new tab.

Browse all PubMed citations for “Natto”

This content is provided for informational purposes only and does not constitute medical advice. Consult a qualified healthcare provider for personalized dietary guidance.

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