Japan Natto Guide
Natto — whole soybeans fermented with Bacillus subtilis bacteria until they develop a distinctive strong ammonia-like smell and produce long, sticky protein strings when stirred — is one of Japan's most nutritionally significant traditional foods and also its most notorious among international visitors. Deeply embedded in Japanese breakfast culture (eaten over rice with soy sauce and mustard), natto is a fermented superfood with genuinely impressive health research behind it. This guide helps you understand, try, and appreciate this polarizing food.
What Is Natto and How Is It Made
Natto is produced from whole soybeans that are soaked for several hours, steamed until soft, then inoculated with Bacillus subtilis natto bacteria — a naturally occurring soil bacterium that has been cultivated for this purpose in Japan for over 1,000 years. The inoculated soybeans are packed in small containers (traditionally rice straw, now polystyrene or paper) and fermented at approximately 40°C for 18–24 hours. During fermentation, the bacteria produce three notable substances: nattokinase, a fibrinolytic enzyme that dissolves fibrin blood clots; polyglutamic acid, the sticky polymer responsible for natto's characteristic long strings; and vitamin K2 (specifically MK-7), a form of vitamin K with superior bioavailability compared to the K1 found in leafy vegetables. The smell produced — often described as reminiscent of strong cheese, ammonia, or fermented straw — is primarily from pyrazines formed during fermentation; it is most intense when the container is first opened and diminishes substantially when stirring distributes the gases. Natto is sold refrigerated in single-serving packages (typically 40–50g per container, two or three containers per retail pack) at every Japanese convenience store, supermarket, and many vending machines, at prices ranging from ¥40 to ¥80 per package. The beans are consumed within 1–2 weeks of production; refrigeration slows but does not stop the fermentation, and older natto develops a stronger flavour and denser texture.
How to Eat Natto Properly
The traditional Japanese method of preparing natto before eating is straightforward though subject to vigorous debate about the optimal technique. Open the small polystyrene container, discard or retain the thin plastic film covering the beans, and add the included soy sauce and mustard packets (typically one small packet of each). Stir the beans vigorously with chopsticks — the recommended rotation count varies from 50 to over 100 in popular culture, though there is no scientific consensus that more stirring improves the flavour; stirring does visibly extend the sticky strings and aerate the mixture. Spoon the prepared natto over a bowl of hot cooked Japanese short-grain rice, ideally fresh and slightly warm. The heat of the rice softens the beans slightly and the contrast of temperatures is part of the eating experience. Optional additions that pair well: a raw egg yolk (particularly popular in Tohoku and Kanto regions), finely sliced green onion (negi), freshly grated daikon radish (reduces the intensity of the smell according to food scientists), shiso leaves, or kimchi. Natto is also widely eaten in other forms: natto maki sushi (natto + pickled daikon + cucumber inside a thin rice roll, sold at every sushi restaurant), natto on toast (popular for breakfast among younger Japanese), natto pasta (particularly in Tokyo), and mixed into miso soup. For visitors trying natto for the first time, natto maki is strongly recommended over eating natto straight — the rice, nori seaweed, and pickled daikon significantly moderate both the smell and texture.
Health Benefits of Natto
Natto's nutritional profile is genuinely exceptional and has been the subject of substantial scientific research since the isolation of nattokinase in 1980 by Dr. Hiroyuki Sumi at the University of Chicago. Nattokinase is a serine protease enzyme with demonstrated fibrinolytic (blood clot-dissolving) activity in human blood; multiple clinical trials have shown that oral nattokinase supplement consumption reduces markers of clotting factor activity and blood viscosity. Vitamin K2 content is extraordinary: natto contains approximately 870 micrograms per 100g in the MK-7 form, the highest concentration of any natural food source and far exceeding the daily adequate intake of 75–120 micrograms; vitamin K2 (specifically MK-7) activates proteins involved in both calcium deposition in bones and calcium removal from arterial walls, with demonstrated associations with reduced cardiovascular calcification and improved bone density in population studies. Probiotic bacteria: Bacillus subtilis natto survives gastric acid conditions that destroy Lactobacillus species, colonizing the large intestine and producing secondary metabolites with antimicrobial properties. Complete protein: natto provides all nine essential amino acids at approximately 16g protein per 100g, comparable to meat. A 2022 population study from Yamagata Prefecture found natto consumption to be independently inversely correlated with mortality from cardiovascular causes after controlling for confounding factors. Important caution: nattokinase has documented anticoagulant interactions — people taking warfarin or other anticoagulant medications should not consume nattokinase supplements and should consult a doctor before significantly increasing dietary natto consumption.
Regional Natto Varieties
Japan produces several distinct natto types and has a well-developed regional natto culture centred on Ibaraki Prefecture. Ibaraki Prefecture (水戸市, Mito City) is considered Japan's natto capital, producing approximately 60% of Japan's commercial natto and hosting an active regional competition and promotion culture — Mito's mascot character, promotional packaging, and tourism marketing all feature natto prominently. The traditional hikiwari natto (挽き割り納豆) uses soybeans that are split or crushed before fermentation rather than left whole; hikiwari has a more intense concentrated flavour per bite, finer texture, and is particularly popular in sushi applications. Kyoto-style natto tends toward lighter fermentation and milder character — consistent with Kyoto's general culinary preference for subtlety. Yamagata Prefecture produces yukiwari natto (雪割り納豆), a traditional variety mixed with salted vegetables (particularly daikon radish) and koji mould, creating a complex fermented combination more similar to a condiment than a standalone food. Niigata Prefecture has developed engineered low-odour varieties using specific Bacillus subtilis strains that produce less pyrazine — marketed to consumers who want natto's nutritional benefits without the characteristic smell. The Natto Museum (納豆博物館) in Mito offers tastings of 20+ variety comparisons and demonstrates the historical development of natto production. The persistent cultural fault line in Japan: Kanto and Tohoku regions consume natto at very high rates (surveys consistently show 80%+ eat natto regularly); Kansai (Osaka, Kyoto, Kobe) has notably lower consumption, and Osaka in particular is associated in popular culture with natto resistance.
Where to Try Natto
Natto is available at virtually every food service context in Japan — it is among the most ubiquitous Japanese foods. Breakfast at any business hotel in Japan (APA Hotel, Toyoko Inn, Dormy Inn, and equivalent properties) includes natto as a standard buffet option alongside rice, miso soup, grilled fish, and rolled omelette. Convenience store chains (7-Eleven, Lawson, FamilyMart) sell single-serving natto packages (¥40–80) in their refrigerated sections, ready to eat with included sauce and mustard packets. The gyudon (beef bowl) chains Yoshinoya, Matsuya, and Sukiya all offer natto as a ¥50–80 additional topping option on any bowl, making them convenient for trying natto in a familiar rice context. Sushi restaurants throughout Japan serve natto maki (¥120–180 per roll) — this is the lowest-commitment and generally most accessible first natto experience for hesitant visitors. In Tokyo, a dedicated Natto Café exists in Akihabara where a specialist menu of natto preparations (natto pasta, natto curry, natto ice cream) is served alongside traditional natto over rice options. Avoiding common mistakes: natto's smell intensifies dramatically when heated in an enclosed space (microwave or steamer) — eating natto at room temperature or over hot rice (where it is not itself being heated) avoids the smell becoming overwhelming in a shared space.
Natto and the East-West Japan Divide
Japan's most consistent and deeply ingrained food culture divide is natto preference, which maps almost exactly onto the historical boundary between eastern (Kanto, Tohoku, Hokkaido) and western (Kansai, Chugoku, Shikoku, Kyushu) Japan. Annual surveys by Japan's food industry associations consistently show that over 80% of adults in Tohoku and Kanto eat natto at least weekly, while equivalent figures in the Kansai region drop to 30–40%. Within this regional divide, Osaka specifically has cultural identity invested in not liking natto — jokes about Osaka residents refusing natto are a standard comedic device in national variety television. The historical explanation is primarily climatic: Bacillus subtilis natto fermentation occurs naturally and reliably in the cooler temperatures and specific humidity of eastern Japan, while fermentation was historically less controlled in western Japan's warmer, more variable climate, making natto production less established as a food tradition there. The cultural reinforcement of this geographic division now exceeds any practical food-access explanation — natto is freely available throughout Japan, but the taste preference and cultural identification with eating or not eating natto remains a reliable east-west marker. Japanese surveys consistently show that natto is among the foods Japanese people most want to share with international visitors (alongside sushi, ramen, and wagashi confectionery) and simultaneously the food they most frequently report receiving negative reactions to when sharing with foreigners — a cultural paradox that has been discussed extensively in Japanese media.
Frequently Asked Questions
Does natto really smell that bad?
The smell is real but often exaggerated. The intensity is highest when the package is first opened; it decreases substantially after stirring and is much less noticeable while actually eating. The smell is similar to strong fermented cheese or certain European deli items — distinctive and initially surprising but not physically overwhelming. Most first-time tasters report that the texture (sticky, stringy) is more of a barrier than the smell. Starting with natto maki sushi significantly reduces both smell and texture barriers.
Can I buy natto outside Japan?
Yes — natto is sold in Japanese and Korean grocery stores in most major cities worldwide and through online food retailers. The most commonly available international variety is the frozen Miyasaka brand (from Ibaraki) which ships well. Refrigerated fresh natto is only reliably available in cities with substantial Japanese populations (New York, Los Angeles, London, Sydney). The flavour profile of fresh natto sold in Japan differs from the frozen export versions, which tend to be milder as the fermentation has progressed less.
Is natto suitable for vegans and vegetarians?
Natto itself is fully plant-based — soybeans plus bacteria with no animal-derived ingredients. The included sauce packets are typically soy sauce (vegan) and mustard (vegan). However, some commercially prepared natto dishes (natto maki sushi, natto over rice at restaurants) may include non-vegan accompaniments like raw egg or fish-based dashi stock. Pure natto from the package eaten over rice with the included condiments is fully vegan. Natto is among the highest-protein plant-based foods available, making it particularly valuable for vegetarian travellers in Japan.
What is the recommended first approach for trying natto?
Natto maki (natto sushi roll) is the most accessible introduction: the nori (seaweed), rice, pickled daikon, and cucumber in the roll moderate both the smell and the stringy texture, and the portions are small enough to stop if you dislike it. The second recommended approach is natto at a hotel breakfast buffet: add a small amount of prepared natto to a bowl of rice alongside other breakfast items so the flavour integrates. Avoid eating natto on its own as your first experience — the concentrated smell and texture without supporting flavours is more challenging than natto as part of a meal.
Where can I buy the best natto in Japan?
For quality natto, specialty stores in Mito (Ibaraki Prefecture) carry artisan producers unavailable at convenience stores. In Tokyo, the Isetan Food Hall in Shinjuku and Takashimaya Times Square in Shinjuku stock premium natto from multiple regional producers. Convenience stores carry perfectly adequate everyday natto — Lawson's private-label natto and 7-Eleven's in-house brand are reliable midrange options. For hikiwari (crushed) natto specifically associated with sushi applications, look for the Oume brand or Mito-grown varieties at supermarkets in eastern Japan.