Natto, Cheonggukjang, and Fermented Foods Made with Bacillus Subtilis

Fermented Foods Natto — scientific infographic poster

Humans have fermented soybeans and legumes with Bacillus subtilis for over a thousand years, long before anyone knew what a bacterium was. The result — sticky, pungent, intensely flavored foods like Japanese natto and Korean cheonggukjang — turns out to be one of the richest natural sources of vitamin K2 and nattokinase ever documented. These are not acquired tastes for everyone, but the science behind them is genuinely impressive.

Table of Contents

  1. Natto: History and Production
  2. Vitamin K2 (Menaquinone-7) Content
  3. Nattokinase: The Fibrinolytic Enzyme
  4. Cheonggukjang and Korean Fermented Soybean Foods
  5. How Natto Is Made at Home
  6. Flavor Profile and How to Eat Natto
  7. Other Global B. subtilis Fermented Foods
  8. Warfarin Interaction Warning
  9. Key Research Papers
  10. Connections
  11. Featured Videos

Natto: History and Production

Natto (納豆) is a traditional Japanese food made from soybeans fermented with Bacillus subtilis var. natto, a subspecies selected over centuries specifically for food use. Historical records place natto in Japan as early as the Heian period (794–1185 CE), with one origin story crediting the warrior Minamoto no Yoshiie, whose soldiers reportedly discovered the transformation when boiled soybeans left in straw wrappings began to ferment in the warmth of a camp.

That origin story matters more than folklore: rice straw in traditional Japan was naturally colonized by B. subtilis, and steamed soybeans wrapped in straw at body temperature (around 40°C) fermented spontaneously. Today, commercial production uses pure B. subtilis var. natto starter cultures instead of straw, but the core process is the same:

  1. Soybeans are soaked in water for 12–18 hours.
  2. They are steamed or pressure-cooked until soft but intact.
  3. A liquid suspension of B. subtilis var. natto spores is sprayed or mixed in at roughly 107 colony-forming units per gram of soybean.
  4. The inoculated beans are packed in small containers (traditionally straw bundles, now polystyrene cups) and incubated at 38–42°C for 16–24 hours.
  5. After fermentation, natto is refrigerated for 24–48 hours to develop its characteristic sticky mucilage (poly-glutamic acid, a polymer produced by the bacteria) and deepen its flavor.

Japan produces approximately 100,000 metric tons of natto annually, and it is consumed mainly in eastern Japan, particularly the Kanto region around Tokyo. Regular consumption is one to three 50 g packs per day.

Vitamin K2 (Menaquinone-7) Content

No food on Earth comes close to natto as a source of vitamin K2 in the menaquinone-7 (MK-7) form. A 100 g serving of natto contains approximately 800–1,000 micrograms (mcg) of menaquinone-7 (MK-7), compared with roughly 0–2 mcg of menaquinone-7 per 100 g in hard cheeses such as Gouda, Edam and Cheddar — the richest everyday Western source of vitamin K2, which carry about 25–75 mcg of total K2 per 100 g, mostly as MK-8 and MK-9 rather than menaquinone-7 (Vermeer 2018). To put that in context, the adequate intake for vitamin K is 90–120 mcg per day for adults — a single 40 g serving of natto (roughly 320–400 mcg of menaquinone-7) supplies about three to four days' worth of that amount.

Why does this matter? Vitamin K2 menaquinone-7 is distinct from vitamin K1 (phylloquinone) found in leafy greens. K1 is primarily directed to the liver for clotting factor synthesis. Menaquinone-7 has a much longer half-life in blood (approximately 72 hours versus 1–2 hours for K1) and accumulates in tissues outside the liver — specifically in bone and arterial walls — where it activates two critical proteins:

Epidemiological data from the Rotterdam Study (4,807 Dutch adults followed for about 7–10 years) found that the highest intake of K2 — but not K1 — was associated with a 57% lower risk of dying from coronary heart disease and significantly lower aortic calcification scores. Menaquinone-7 specifically, because of its longer half-life, appears more effective per microgram than shorter-chain menaquinones like menaquinone-4 (MK-4).

Nattokinase: The Fibrinolytic Enzyme

During fermentation, B. subtilis var. natto secretes a serine protease enzyme called nattokinase (also designated subtilisin NAT or SUBS1). This enzyme was first characterized in 1987 by Dr. Hiroyuki Sumi and colleagues at the Department of Physiology, Miyazaki Medical College, Japan, who reported a strong clot-dissolving (fibrinolytic) activity in natto and named the enzyme nattokinase. The commonly told account places Sumi's first observation of natto dissolving fibrin earlier, at the University of Chicago.

Nattokinase dissolves fibrin clots directly (it cleaves fibrin strands) and also stimulates the body's own fibrinolytic system by degrading plasminogen activator inhibitor-1 (PAI-1) and activating tissue plasminogen activator (t-PA). In laboratory models, nattokinase has been shown to:

Human clinical research is growing but still early. Nattokinase is also widely promoted for cholesterol, and people who take it report using it for that purpose. One study found modest reductions in blood pressure after 8 weeks of nattokinase supplementation.

Important limitation: Nattokinase is not U.S. Food and Drug Administration-approved as a drug, and most human trials have been small. Nattokinase from food sources (natto itself) does survive gastric digestion to some extent — animal studies confirm measurable fibrinolytic activity in the blood after oral natto consumption — but the effective dose from food versus supplements differs. Because nattokinase breaks down fibrin, the protein that holds blood clots together, it could add to the bleeding risk of people with bleeding disorders, people taking blood thinners (anticoagulants), and people having surgery.

Cheonggukjang and Korean Fermented Soybean Foods

Korea has its own B. subtilis-fermented soybean tradition, which produces a family of foods with overlapping but distinct characteristics:

Cheonggukjang (청국장) is the closest Korean equivalent to natto. Soybeans are boiled, then fermented at 40–45°C for 2–3 days — a shorter fermentation window than doenjang. The result is a pasty, sticky product with a notably pungent ammonia aroma, similar to natto. Cheonggukjang is typically used in a thick, salty stew (cheonggukjang jjigae) with kimchi, tofu, and vegetables. It is less processed and considered more nutritionally potent than long-fermented pastes.

Laboratory analyses of cheonggukjang have confirmed the presence of nattokinase-like fibrinolytic enzymes produced by B. subtilis strains native to Korean fermentation environments. One study isolated 11 B. subtilis strains from traditional cheonggukjang with fibrinolytic activity comparable to commercial nattokinase preparations.

Doenjang (된장) is a fermented soybean paste more similar in appearance to Japanese miso, but made without rice or barley grain additions and fermented for months to years. The extended aging and different microbial ecology (including molds) results in lower concentrations of nattokinase and menaquinone-7 compared to cheonggukjang, but doenjang retains significant quantities of isoflavones, short-chain peptides, and bioactive compounds associated with its own health research portfolio, including blood pressure reduction in hypertensive rats and anti-inflammatory effects in cell culture models.

South Korean per-capita consumption of fermented soybean products is among the highest in the world, and epidemiological comparisons between Korean and Western populations have prompted research into whether these foods contribute to the relatively lower rates of cardiovascular mortality historically observed in Korea — though diet, lifestyle, and genetic factors all interact.

How Natto Is Made at Home

Home natto makers manage with modest equipment. The key inputs are dry soybeans, a B. subtilis var. natto starter culture (sold online in freeze-dried form), and a way to hold about 40°C for 24 hours; home makers use a yogurt maker, an electric pressure cooker with a yogurt setting, or a warm oven with the light on.

The usual home procedure:

  1. Soak: 250 g of dry soybeans are rinsed, covered with 3× their volume of cold water and soaked for 18–24 hours (they roughly double in size).
  2. Cook: The beans are drained and pressure-cooked for 20–25 minutes at high pressure, or steamed for 3–4 hours, until a bean squishes easily between the fingers without feeling grainy inside. Undercooked beans inhibit fermentation, so the beans are cooked fully.
  3. Inoculate: While still hot (above 70°C), the beans go into a sterilized bowl and are left to cool to about 50°C (hotter than that kills the starter). A small amount of natto starter (typically 0.1 g per 250 g beans, following the starter's own instructions) is dissolved in 2 tablespoons of sterile warm water, poured over the beans and mixed in thoroughly with a sterilized spoon.
  4. Ferment: The beans are spread in a shallow, sterilized tray to a depth of about 2 cm, covered loosely with plastic wrap (with holes poked in it for gas exchange) or a clean cloth, and kept warm at 38–42°C for 20–24 hours.
  5. Check: After 20 hours, a good batch shows a white powdery surface film (the bacterial growth layer) and the characteristic sticky strings when a bean is pulled away with a fork. A strong, ammonia-forward smell is normal.
  6. Age: The natto is refrigerated for 24–48 hours before eating. This rest period develops fuller flavor, softens the ammonia edge slightly, and allows the poly-glutamic acid mucilage to fully set.

What home makers report: Cleanliness matters more than sterility — the main risk is mold contamination if fermentation temperature is too low or beans sit wet. Green, black, or pink mold is a sign of a spoiled batch, and home makers throw such a batch away. Many find a yogurt maker with a removable tray set to 40°C the most reliable home setup. Small-batch experimenters often find that storing natto in individual single-serving portions and freezing any excess preserves flavor and enzyme activity well for up to 3 months.

Flavor Profile and How to Eat Natto

Natto is polarizing, and it is worth being honest about that. First-timers frequently describe three sensory challenges: the stringy, mucilaginous texture (the poly-glutamic acid threads stretch several centimeters), a pungent ammonia-and-fermented-soy smell reminiscent of aged cheese pushed to the extreme, and a bitter aftertaste with a faint earthiness. People either adapt to it within a few tries or find it genuinely difficult to tolerate, and both responses are normal.

Traditional Japanese serving: A small pack of natto (approximately 40–50 g) is served over a bowl of steamed short-grain rice, with the following added in the package or alongside:

The beans are stirred vigorously before serving — some practitioners insist on 50+ stirs — which develops and aerates the sticky threads and blends the seasonings. Many Japanese people eat natto at breakfast.

Making it more approachable: For newcomers, mixing natto with a raw egg yolk softens the texture considerably. Adding kimchi masks the ammonia note with fermented spice. Natto toast with avocado and a drizzle of ponzu is popular in Japanese-American communities as an introduction. Many newcomers find that starting with small amounts (one tablespoon) on rice and building tolerance gradually works better than eating a full pack on the first attempt.

Frozen natto is widely sold in Japanese grocery stores and retains most of its vitamin K2 and nattokinase activity after thawing. Heating natto above approximately 70°C will denature nattokinase, so adding it to dishes after cooking or serving it cold over hot rice preserves the enzyme.

Other Global B. subtilis Fermented Foods

The discovery that fermenting legumes with B. subtilis creates edible, protein-rich, shelf-stable food appears to have occurred independently in multiple cultures across Asia and Africa:

Kinema — Made in Nepal, India's Sikkim and Darjeeling regions, and parts of Bhutan. Soybeans (or sometimes other legumes) are boiled and wrapped in fern leaves or bamboo, then fermented at ambient temperatures for 2–3 days. The resulting product has a sticky texture and strong smell similar to natto. B. subtilis is consistently the dominant fermenting organism. Kinema is typically used in curries and stews and is an important protein source in highland communities where refrigeration and meat are scarce.

Thua nao — A traditional fermented soybean product of northern Thailand and parts of Myanmar. Soybeans are cooked and fermented in banana leaves for 2–3 days. The final product is pressed into flat discs and sun-dried for preservation. B. subtilis strains are the primary fermenting organisms. Thua nao is used as a flavoring paste (similar to miso or soybean paste) in local dishes. Studies have confirmed fibrinolytic activity in thua nao comparable to natto, though menaquinone-7 content data are limited.

Dawadawa (also called sumbala, iru, or locust bean seasoning) — Made across the Sahel and West Africa (Ghana, Nigeria, Burkina Faso, Senegal, and others) from the seeds of the African locust bean tree (Parkia biglobosa). Seeds are boiled, dehulled, and fermented in sealed pots for 2–4 days at ambient tropical temperatures. B. subtilis and related Bacillaceae dominate the fermentation. Dawadawa is used as a flavor-enhancing condiment — a small ball of it is added to soups and stews much like a bouillon cube — and is a critical source of protein, riboflavin, and essential amino acids for populations with limited access to animal protein. Research has confirmed nattokinase-like fibrinolytic enzymes in dawadawa extracts.

The convergent independent discovery of B. subtilis-fermented legumes on three continents reflects how well-suited this bacterium is to warm, protein-rich, anaerobic environments — and how universal the nutritional challenge of preserving and concentrating plant protein has been across human history.

Warfarin Interaction Warning

This is the most clinically important safety note on this page: the very large amount of vitamin K in natto can weaken the effect of warfarin and other vitamin K-sensitive blood thinners (anticoagulants). The U.S. warfarin label lists increased vitamin K intake as a cause of a lower INR response, and it advises people taking warfarin to eat a normal, balanced diet with a consistent amount of vitamin K and no drastic changes in eating habits.

A range bar for the INR blood test: the therapeutic range of 2.0 to 3.0 sits between a below-range zone where stroke risk rises and an above-range zone, with an arrow showing a patient on a stable warfarin dose falling from 2.5 to 1.1 within 48 hours of eating natto, because one serving carries 800 to 1,000 mcg of vitamin K2 with a half-life of about 72 hours. NATTO AND WARFARIN: THE INR DROP INR blood test · a patient on a stable warfarin dose 1.1 2.0 2.5 3.0 below range stroke risk rises therapeutic range typically 2.0–3.0 above range overshoot 2.5 → 1.1 within 48 hours of natto stable dose after natto INR (International Normalized Ratio) → case reports cited on this page · the stroke risk is for atrial fibrillation or a mechanical heart valve WHY ONE SERVING 800–1,000 mcg of K2 in a 100 g serving of natto half-life ~72 hours elevated three days or more; spinach K1 clears in hours it feeds what warfarin blocks clotting factors II, VII, IX, X consistent intake can be managed; some weeks on, some off makes INR very difficult to control

Warfarin works by blocking vitamin K-dependent clotting factor synthesis (factors II, VII, IX, X, and proteins C and S). The therapeutic dose is calibrated against a patient's baseline vitamin K intake, monitored via the International Normalized Ratio (INR) blood test. When vitamin K intake changes dramatically, the warfarin dose that was keeping international normalized ratio in the therapeutic range (typically 2.0–3.0) may suddenly undershoot or overshoot.

A single 100 g serving of natto contains 800–1,000 mcg of vitamin K2 as menaquinone-7. Menaquinone-7's long half-life (approximately 72 hours) means that a single serving of natto can significantly elevate circulating vitamin K2 for three days or more — far longer than the K1 in a plate of spinach, which clears in hours. Case reports in the literature document dramatic international normalized ratio drops (from therapeutic 2.5 to subtherapeutic 1.1) within 48 hours of natto consumption in patients on stable warfarin doses. A subtherapeutic international normalized ratio in a patient with atrial fibrillation or a mechanical heart valve raises the risk of stroke.

What this means in practice:

For people not on anticoagulants, high vitamin K2 intake from natto has not been shown to cause hypercoagulation in healthy individuals — the body's clotting cascade has sufficient regulatory mechanisms to prevent this in the absence of drug interference.

Key Research Papers

  1. Sumi H et al. A novel fibrinolytic enzyme (nattokinase) in the vegetable cheese Natto; a typical and popular soybean food in the Japanese diet. Experientia. 1987. — PubMed PMID: 3478223
  2. Geleijnse JM et al. Dietary intake of menaquinone is associated with a reduced risk of coronary heart disease: the Rotterdam Study. J Nutr. 2004. — PubMed PMID: 15514282
  3. Vermeer C, Raes J, van 't Hoofd C, Knapen MHJ, Xanthoulea S. Menaquinone content of cheese. Nutrients. 2018;10(4):446. — PubMed PMID: 29617314
  4. Kurosawa Y et al. A single-dose of oral nattokinase potentiates thrombolysis and anti-coagulation profiles. Sci Rep. 2015. — PubMed PMID: 26109079
  5. Sato T et al. Comparison of menaquinone-4 and menaquinone-7 bioavailability in healthy women. Nutr J. 2012. — PubMed PMID: 23140417
  6. Jensen GS et al. Consumption of nattokinase is associated with reduced blood pressure and von Willebrand factor: a randomized, double-blind, placebo-controlled, multi-center North American clinical trial. Integr Blood Press Control. 2016. — PubMed PMID: 27785095
  7. Ren NN et al. A clinical study on the effect of nattokinase on carotid artery atherosclerosis and hyperlipidaemia. Zhonghua Yi Xue Za Zhi. 2017. — PubMed PMID: 28763875
  8. Yatagai C et al. Nattokinase-promoted tissue plasminogen activator release from human cells. Pathophysiol Haemost Thromb. 2008. — PubMed PMID: 19996631
  9. Fujita M, Ohnishi K, Takaoka S, Ogasawara K, Fukuyama R, Nakamuta H. Antihypertensive effects of continuous oral administration of nattokinase and its fragments in spontaneously hypertensive rats. Biol Pharm Bull. 2011;34(11):1696-1701. — PubMed PMID: 22040882

Back to Table of Contents

Connections

Back to Table of Contents