Natto: The Fermented Soybean Probiotic Superfood of Japan, source of Vitamin K2 MK-7

Natto is a traditional Japanese fermented soybean food produced by the action of Bacillus subtilis var. natto. Known for its powerful pungent aroma, sticky slimy texture, and unique umami flavor, natto is one of the most distinctive functional foods in Japanese cuisine. Unlike other fermented soybean products that use salt or koji mold, natto relies on alkaline fermentation through Bacillus species. It is most commonly eaten as a breakfast food served over steamed rice. The word natto derives from nattō, where natto refers to the fermentation process and the final product.

Cultural Roots, Varieties, and Regional Context

Cultural Origins

Natto has been consumed in Japan for over a thousand years. Historical records suggest the fermentation method may have arrived from China alongside Buddhism. The traditional production method involved wrapping cooked soybeans in rice straw, which naturally harbored Bacillus subtilis spores. During the Taisho Period from 1912 to 1926, scientists developed a method to cultivate Bacillus natto in the laboratory without the need for straw, allowing for reliable industrial scale production.

The fermentation of soybeans by Bacillus subtilis produces a musty flavor, a slimy appearance, and a distinct odor created by sticky viscous polymers. These polymers contain several compounds including glutamic acid, amino acids, and fructan. In Japanese households, natto is traditionally presented with mustard, seaweed, finely sliced onion, and a small amount of soy sauce, served together with steaming rice.

Classification of Natto Varieties

Natto is classified into three main types:

Itohiki natto (stringy natto)

This is the most common variety consumed in Japan today. It is produced by inoculating steamed soybeans with Bacillus subtilis natto and fermenting for approximately 24 hours without the addition of salt. The characteristic sticky, stringy texture results from poly gamma glutamic acid (PGA) production. This variety is typically sold in polystyrene foam boxes accompanied by small packets of mustard and tsuyu (soy based condiment).

Hama natto (Hamamatsu natto)

This variety differs fundamentally from itohiki natto in both production method and final product characteristics. Steamed soybeans are fermented with koji mold, then aged in saltwater for 12 to 15 months, and finally dried in sunlight. The only ingredients are soybeans, salt, and ginger. No other seasonings are added. The umami becomes condensed in the soybeans solely through the power of fermentation and aging. The flavor is similar to miso or soy sauce but deeper and richer. Hama natto is said to have been a favorite of Tokugawa Ieyasu, the first shogun of the Tokugawa Shogunate. Its long shelf life and portability made it valued as a protein source during battles.

Daitokuji natto (temple natto)

This variety is prepared by inoculating soybeans with koji mold, followed by aging for 4 to 6 months with the addition of salt. It represents an older style of natto production originating in Buddhist temples.

Regional Consumption Patterns

Eating natto as a daily custom is less popular in the Kansai region compared to eastern Japan. Whether natto is popular or not depends significantly on region within the country.

Microbiology and Probiotic Profile

Primary Fermenting Organism

Bacillus subtilis var. natto (also known as Bacillus natto) is the bacterium responsible for natto fermentation. This Gram positive, rod shaped bacterium typically measures 2 to 6 micrometers in length and less than 1 micrometer in width. The optimal temperature for growth is 30 to 35 degrees Celsius, allowing for a doubling time of approximately 20 minutes. Under starvation conditions, cells undergo a complex two cell division resulting in endospore formation, with spores discharged by lysis of the surrounding mother cell.

Bacterial Load and Probiotic Counts

Total Bacillus count in fresh natto

The fermentation process results in Bacillus subtilis natto reaching concentrations of approximately 10⁸ to 10⁹ CFU per gram. One study documented survival densities of 7.87 log CFU per milliliter after exposure to bile salts and 6.73 log CFU per milliliter after pH 2 exposure.

Spore formation

A key characteristic of Bacillus subtilis natto is its ability to form endospores. These spores demonstrate remarkable resilience. Research in dairy cows showed that spores increased during the first 24 hours of rumen fermentation with survival rates reaching 191.3 percent at 24 hours and 175.9 percent at 72 hours. The spores can survive in simulated gastric conditions at pH 2.5 with 0.3 percent pepsin, maintaining 83.31 percent viability after 3 hours. However, the spores cannot permanently colonize the gastrointestinal tract and are typically cleared within 48 hours.

Peak Probiotic Diversity and Count Stage

The peak of probiotic activity and Bacillus population occurs at the completion of the fermentation period, typically after 18 to 24 hours of incubation at 40 to 45 degrees Celsius. At this stage:

Bacillus subtilis natto populations reach maximum concentration between 10⁸ and 10⁹ CFU per gram

Poly gamma glutamic acid (PGA) production is at its highest level, giving the characteristic stringy texture

Nattokinase enzyme activity is maximized

The full complement of bioactive compounds including vitamin K2 (menaquinone-7) and polyamines reaches peak levels

After this stage, the product is immediately refrigerated to slow further metabolic activity. Fresh natto is consumed within a few days, though it can be stored frozen for extended periods.

Probiotic Properties Documented

Research has confirmed multiple probiotic characteristics of Bacillus subtilis natto:

Bile salt tolerance: After 3 hours in 0.3 percent bile salt containing media, survival reached 96.8 percent of initial density corresponding to 7.87 log CFU per milliliter. In 0.6 percent bile salt, survival reached 85.5 percent corresponding to 6.95 log CFU per milliliter.

Acid tolerance: After 3 hours exposure to pH 2, bacterial survival density reached 6.73 log CFU per milliliter, representing 79.11 percent of initial density.

Gastric fluid tolerance: In simulated gastric conditions at pH 2.5 with 0.3 percent pepsin, survival density reached 6.71 log CFU per milliliter, representing 83.31 percent of initial density.

Antimicrobial activity: Bacillus subtilis natto demonstrates antibacterial activity against four pathogenic bacteria with zones of inhibition measured at 8.0 millimeters for Escherichia coli, 9.0 millimeters for Salmonella typhimurium, 10.0 millimeters for Staphylococcus aureus, and 8.0 millimeters for Pseudomonas aeruginosa.

Preparation Guidelines

Raw Materials

Soybeans

Quantity: 500 grams. Small sized soybeans are preferred for natto production as they ferment more evenly.

Water

Quantity: Sufficient for washing, soaking, and steaming

Bacillus subtilis natto starter culture

Quantity: Commercial natto starter or 10 grams of high quality frozen natto from a previous batch

Equipment

Steamer or pressure cooker, sterilized glass or plastic containers with lids, incubator or warm place maintaining 40 to 45 degrees Celsius

Traditional Preparation Process

Step 1: Soybean selection and washing

Select whole, unbroken small soybeans. Wash thoroughly under running water to remove any dirt or damaged beans.

Step 2: Soaking

Soak the cleaned soybeans in three times their volume of water for 12 to 18 hours. The soaking time varies with ambient temperature; longer soaking is required in colder conditions. The beans should absorb water and approximately double in size.

Step 3: Steaming

Drain the soaked beans thoroughly. Steam the soybeans under pressure using a pressure cooker at 0.98 to 1.47 bar vapor pressure for 20 to 30 minutes. Alternatively, steam at atmospheric pressure for 2 to 3 hours. The beans should become soft enough to be mashed between fingers. Proper steaming is critical as it denatures soybean proteins, inactivates trypsin inhibitors, and creates an environment suitable for Bacillus growth.

Step 4: Cooling

Cool the steamed soybeans to approximately 45 degrees Celsius. Do not allow the beans to cool below 40 degrees Celsius before inoculation. Overcooling can allow competitive microbes to establish.

Step 5: Inoculation

Sprinkle the Bacillus subtilis natto starter culture over the cooled beans. For those using commercial frozen natto as starter, mash the frozen natto and mix with a small amount of steamed beans before combining with the full batch. Mix thoroughly to ensure even distribution of the bacteria.

Step 6: Fermentation

Transfer the inoculated beans into sterilized containers, spreading them in a layer no more than 5 centimeters deep. Cover with a clean cloth or perforated lid to allow airflow while preventing contamination. Maintain the containers at 40 to 45 degrees Celsius for 18 to 24 hours. An incubator, a yogurt maker, or a warm place near a heater can serve this purpose. During fermentation, avoid disturbing the beans.

Step 7: Checking doneness

Properly fermented natto develops a white to grayish coating over the beans. When stirred, the beans should produce abundant sticky, stringy threads. A strong ammonia like, musty aroma indicates successful fermentation. The beans should be soft and easily mashed.

Step 8: Aging and refrigeration

After fermentation is complete, transfer the natto to the refrigerator at 4 degrees Celsius and age for 24 to 48 hours. This cold aging step allows the flavors to mellow and the texture to develop fully. Refrigerated natto typically remains good for 5 to 7 days. For longer storage, natto can be frozen for several months without significant quality loss.

Medicinal and Nutraceutical Benefits

Natto offers a remarkable range of health benefits derived from both live probiotics and the unique bioactive compounds generated during fermentation.

Bone Health via Vitamin K2 (Menaquinone-7)

Natto is the richest natural source of menaquinone-7 (MK-7), a form of vitamin K2 involved in osteocalcin activation and bone mineralization. Natto contains approximately 100 times more menaquinone-7 than most cheeses.

A meta analysis of Japanese studies involving 2,327 participants documented significant effects of habitual natto consumption:

Serum MK-7 levels: Natto intake is associated with significantly elevated serum MK-7 levels. After sensitivity analysis removing an outlier, the effect size was 2.10 with a 95 percent confidence interval of 1.55 to 2.66.

Osteocalcin carboxylation: Increased carboxylated osteocalcin (OC) with an effect size of 0.26 and confidence interval of 0.08 to 0.43. Decreased undercarboxylated osteocalcin (ucOC) with an effect size of -0.50 and confidence interval of -0.74 to -0.26.

Bone mineral density: Modestly greater bone mineral density across skeletal sites with an effect size of 0.65 and confidence interval of 0.09 to 1.21. Sensitivity analysis refined this to 0.35 with confidence interval of 0.21 to 0.48.

These findings suggest natto may represent a culturally grounded dietary approach for supporting bone health and osteoporosis prevention, though generalizability beyond Japanese populations warrants further investigation.

Cardiovascular Benefits via Nattokinase

Nattokinase is a fibrinolytic enzyme produced by Bacillus subtilis natto during fermentation. This enzyme has demonstrated significant blood clot dissolving activity.

Research has documented that culture broth from Bacillus subtilis natto after 36 hours of fermentation has the ability to dissolve 25 percent of fresh clot weight after 2 hours of incubation. This fibrinolytic activity underlies the potential of natto in prevention and treatment of cardiovascular diseases. The bacteria show exceptional bile salt hydrolase activity and cholesterol removal properties.

Liver Health and Fat Metabolism

High poly gamma glutamic acid (γ-PGA) natto has demonstrated beneficial effects on liver lipids. Research in adult female mice fed a 30 percent high γ-PGA natto diet for 28 days revealed:

Liver lipid and triglyceride contents were significantly lower in the high γ-PGA natto group compared to the control group. Amounts of bile acids and lipids in the feces were significantly higher in the natto fed group. Cecal butyric acid concentration was significantly elevated. The ratio of Firmicutes to Bacteroidetes was significantly lower in the natto fed mice. A significantly higher relative abundance of Lachnospiraceae was observed along with significantly lower relative abundance of Coriobacteriaceae.

These findings suggest that high γ-PGA natto is a beneficial dietary component for the prevention of nonalcoholic fatty liver disease (NAFLD).

Polyamine Production

Spermidine is a polyamine with documented anti aging and cardioprotective properties. Research has examined polyamine variation during each step of the natto production process. The steaming process slightly decreases spermidine in soybeans. However, the subsequent fermentation process results in a 41.1 percent increase of spermidine and a 19.4 percent reduction of spermine compared to steamed soybeans. These results indicate that Bacillus subtilis natto produces spermidine during the fermentation process. Spermidine production differs among inoculum strains, suggesting that selection of starter cultures with high spermidine productivity can improve polyamine levels in natto.

Nutritional Composition

Per 100 grams, natto provides 211 calories with the following macronutrient profile:

Protein

19 grams

Fat

11 grams, predominantly polyunsaturated fats which can decrease LDL cholesterol and may reduce risk of heart disease and stroke

Total carbohydrates

13 grams, comprised of 5.4 grams of dietary fiber and 4.9 grams of sugar

Saturated fat

1.6 grams

Micronutrient content per 100 grams is exceptionally rich:

Manganese provides 2.7 milligrams, representing 130 to 134 percent of recommended daily intake. Copper provides approximately 1 milligram (58 percent of daily needs). Iron provides 15 milligrams (84 percent of daily needs). Potassium provides 729 to 1,276 milligrams (36 percent of daily needs). Magnesium provides 201 milligrams (50 percent of daily needs). Calcium provides 217 milligrams. Phosphorus provides 305 milligrams (30 percent of daily needs). Zinc provides 5.3 milligrams (35 percent of daily needs). Selenium provides 15.4 micrograms (22 percent of daily needs). Vitamin C provides approximately 23 milligrams (38 percent of daily needs).

Bioactive Compounds Summary

Nattokinase

A fibrinolytic enzyme that dissolves blood clots and supports cardiovascular health

Vitamin K2 (menaquinone-7)

Supports bone mineralization and arterial health

Gamma polyglutamic acid (γ-PGA)

Provides the characteristic stickiness, functions as a prebiotic, and supports liver health

Soybean isoflavones

Present as aglycones with enhanced bioavailability due to fermentation

Spermidine

A polyamine with anti aging and cardioprotective properties

Usage and Culinary Applications

Traditional Serving Methods

Natto is most commonly eaten as a breakfast food. The typical serving involves opening a packaged container, adding the accompanying mustard and tsuyu sauce, stirring vigorously to develop the sticky strings, and then spooning over hot steamed rice. Stirring is essential as it aerates the product and maximizes the characteristic stringy texture.

Modern Culinary Uses

Natto can be incorporated into various dishes:

Natto donburi combines natto with rice in a bowl, sometimes with additional toppings like raw egg or tuna. Natto sushi is prepared as a hand roll or as a topping for sushi rice. Nattojiru incorporates natto into miso soup as a seasoning. Natto can also be used as a topping for soba noodles, udon noodles, spaghetti, and okonomiyaki.

Natto has found application as a potential food ingredient in various products. It is used to flavor fish, meat, and vegetables. The fermentation process produces proteolysis activity which improves taste and nutritional value by removing unwanted flavors.

Usage Note

Natto has a strong acquired taste profile. First time consumers often find the pungent ammonia like aroma and sticky, slimy texture challenging. Begin with small quantities mixed into rice with plenty of mustard and tsuyu sauce to moderate the flavor. Individuals taking blood thinning medications should consult a healthcare provider before regular natto consumption due to its vitamin K2 content, which can theoretically interfere with warfarin and similar anticoagulants.

Enjoy natto as a protein rich breakfast over steamed rice, as a functional food addition to soups and noodle dishes, or as a unique ingredient in creative culinary applications.