Sticky, pungent, and divisive \u2014 natto is one of Japan’s oldest fermented foods and one of its most misunderstood. Behind the smell and the strings lies a fermentation of extraordinary biological precision, and a food culture that has quietly endured for over a thousand years.<\/p>\n\n\n\n
There is a rule at sake breweries across Japan: do not visit if you have eaten natto that day. The reason is practical and precise. The bacterium responsible for natto’s fermentation \u2014 Bacillus subtilis<\/em> var. natto<\/em>, known in Japanese as natto-kin<\/em> \u2014 is extraordinarily resilient. It can survive on the skin and clothing for hours after contact with the food, and if it finds its way into a sake brewery, it can disrupt the delicate fungal and microbial work of sake production entirely. The warning is not superstition. It is a measure of how alive natto fermentation is, and how insistently it asserts its presence.<\/p>\n\n\n\n That insistence \u2014 the way natto announces itself through smell, through texture, through its stubborn biological vitality \u2014 is both the reason it has been eaten in Japan for over a thousand years and the reason it remains, within Japan itself, a food that people tend to love completely or avoid entirely. A 2009 survey found that approximately seventy percent of Japanese people find natto pleasant to eat. The remaining thirty percent, concentrated largely in western Japan, tend to feel the opposite. The divide between east and west Japan over natto is one of the oldest and most persistent culinary fault lines in the country.<\/p>\n\n\n\n To understand why natto produces such strong responses \u2014 and why it has endured despite them \u2014 it helps to understand what is actually happening inside the beans.<\/p>\n\n\n\n Bacillus subtilis<\/em> var. natto<\/em> is a gram-positive, spore-forming bacterium found naturally in soil and, crucially, on the surface of rice straw. It is aerobic \u2014 it requires oxygen \u2014 and it is thermophilic, meaning it thrives at temperatures higher than most food-fermenting microorganisms prefer. The ideal fermentation temperature for natto is approximately forty degrees Celsius, a warmth that suppresses many competing bacteria while allowing B. subtilis natto<\/em> to dominate the environment entirely.<\/p>\n\n\n\n The bacterium produces several enzymes during fermentation. Proteases break down the proteins of the soybean into amino acids \u2014 including significant quantities of glutamic acid, which is responsible for natto’s pronounced umami flavor. Simultaneously, B. subtilis natto<\/em> synthesizes and secretes poly-gamma-glutamic acid (PGA): a long-chain polymer of glutamic acid molecules that accumulates as a sticky, mucous-like coating on the surface of each bean. This PGA is the source of natto’s characteristic stickiness and its famous threads \u2014 the strings that form when natto is stirred or pulled apart. The longer the strings, the more PGA has been produced; in traditional evaluation, long strings indicate high-quality fermentation. PGA has no taste of its own, but it contributes significantly to natto’s mouthfeel and is increasingly studied for its industrial applications, from biodegradable plastics to drug delivery systems.<\/p>\n\n\n\n The smell \u2014 the compound most responsible for natto’s divisive reputation \u2014 comes primarily from pyrazines and other volatile aromatic compounds produced during fermentation, combined with ammonia released as the bacterium breaks down proteins. The aroma is distinct and unmistakable: earthy, sharp, with a quality that has been described as resembling aged cheese or, less charitably, old socks. To those who have grown up eating natto, this aroma is inseparable from the warmth and comfort of a breakfast bowl of rice. To those encountering it for the first time, it tends to be the primary obstacle.<\/p>\n\n\n\n The precise origin of natto is unknown, and the uncertainty has accumulated several legends over the centuries. The most widely cited places the discovery in the 1080s, during the Gosannen War, when the samurai lord Minamoto no Yoshiie and his army were camped in what is now Ibaraki Prefecture. Surprised by an enemy approach during an evening meal of boiled soybeans, the soldiers quickly wrapped their food in the rice straw they had been using to feed their horses and retreated. Several days later, when the straw bundles were opened, the beans had been transformed: sticky, threaded, and fragrant in a way that was entirely new. According to the legend, the general tasted the transformed beans and approved of them. Natto<\/em> \u2014 beans offered to the general \u2014 became the name of the food.<\/p>\n\n\n\n The legend is plausible, if unverifiable. Rice straw is a natural habitat of Bacillus subtilis<\/em>, and the warmth of bundled straw \u2014 especially when wrapped around beans that had just been cooked \u2014 provides exactly the temperature conditions that the bacterium needs to ferment. Spontaneous fermentation of this kind almost certainly happened many times across Japan’s agricultural history before anyone thought to eat the result rather than discard it. The legend captures the logic of the discovery, if not its exact circumstances.<\/p>\n\n\n\n What is documentable is the timeline of natto’s appearance in the written record. The term natto first appeared in a Japanese document in 1068, referring at that time to a different product \u2014 salt-fermented soy nuggets made with koji mold, a category now called shiokara natto<\/em> or tera natto<\/em>, still produced in some Kyoto temples and distinct from the sticky-fermented natto discussed here. The Muromachi-period text Sh\u014djin gyorui monogatari<\/em> (Tales of Vegetables and Fish) includes a character that personifies natto, evidence that the food was already culturally embedded enough to be personified in fiction. By the Edo period (1603\u20131868), natto was being produced by small-scale manufacturers and sold by street vendors each morning in Edo, as routine a part of urban working-class breakfast as rice and pickles.<\/p>\n\n\n\n For centuries, natto was made the same way the Minamoto legend describes: boiled soybeans wrapped in rice straw bundles, incubated in a warm environment \u2014 the residual heat of a cooking fire, a warm corner of the farmhouse \u2014 and left to ferment for one to two days. The straw provided both the bacterial culture and the insulation. No starter culture was required, because the bacterium was already present on the straw itself. The process was variable and somewhat unpredictable, depending on the bacterial load of the specific straw, the ambient temperature, and the vigilance of whoever was tending the fermentation.<\/p>\n\n\n\n A fundamental change occurred during the Taisho period (1912\u20131926), when researchers succeeded in isolating a pure starter culture of Bacillus subtilis natto<\/em> that could be produced and distributed without the need for straw. This innovation \u2014 the ability to inoculate steamed soybeans with a measured, consistent dose of the fermenting bacterium \u2014 transformed natto from a craft food with inherent variability into something that could be produced at industrial scale with consistent results. The railway expansion of the same period, linking natto’s northeastern heartland with Tokyo, enabled distribution to the capital at a scale previously impossible.<\/p>\n\n\n\n Today, the commercial production of natto follows a precisely controlled sequence. Soybeans \u2014 typically small varieties, chosen because their size allows fermentation to penetrate to the center of the bean more easily \u2014 are washed and soaked for twelve to twenty hours, then steamed for approximately six hours. A measured quantity of B. subtilis natto<\/em> starter is mixed into the cooked beans, which are then packed into their containers and placed in fermentation rooms maintained at forty degrees Celsius for up to twenty-four hours. After fermentation, the natto is cooled and aged in refrigeration for up to one week \u2014 a resting period during which the PGA strings develop fully and the flavor deepens. The entire process, from raw bean to packaged product, takes approximately eight to ten days.<\/p>\n\n\n\n Workers in natto facilities take particular care not to introduce skin bacteria into the fermentation. Even though B. subtilis natto<\/em> is dominant enough to suppress many competing organisms, contamination from human contact can introduce off-flavors and inconsistencies. The care with which natto production is managed reflects an understanding that fermentation, even when controlled, is a biological process \u2014 one that requires attention and respect rather than simply the application of a formula.<\/p>\n\n\n\n The natto most familiar today \u2014 the sticky, threaded, B. subtilis<\/em>-fermented variety \u2014 is technically known as itohiki natto<\/em> (thread-pulling natto), named for the threads that form when the beans are separated. But a different tradition of natto exists alongside it, with a history that may be older.<\/p>\n\n\n\n Shiokara natto<\/em> \u2014 also called tera natto<\/em> (temple natto) \u2014 is made not with Bacillus subtilis<\/em> but with koji mold and salt, producing a dry, deeply savory, dark-colored product that resembles Chinese douchi (fermented black beans) more than modern natto. It is not sticky. It does not thread. Its flavor is dense, concentrated, and umami-forward in a way that reflects its long fermentation with koji enzymes rather than bacterial activity. Temple natto is still produced in several Kyoto temples and in some other regional areas, and it occupies a completely different flavor register from its more famous bacterial cousin.<\/p>\n\n\n\n The existence of these two traditions \u2014 one bacterial, one fungal; one sticky, one dry; one ubiquitous, one rare \u2014 reflects the broader complexity of Japan’s fermentation culture, in which the same raw ingredient (soybeans) can be directed by different microorganisms and different processes toward entirely different destinations.<\/p>\n\n\n\n Within itohiki natto itself, regional variation is significant. Ibaraki Prefecture \u2014 and its largest city, Mito \u2014 is considered the heartland of natto culture. Mito natto, particularly the traditional wara natto still sold wrapped in rice straw at Mito station and in the city’s markets, is regarded as the most authentic expression of the food’s origins. The rice straw wrapping is no longer the source of fermentation in commercial production \u2014 the bacterial starter is added separately \u2014 but it remains the traditional packaging, and the wara gives the finished natto a subtle additional character from the bamboo and plant compounds in the straw itself.<\/p>\n\n\n\n Natto consumption is highest in the Tohoku and Kanto regions, declining significantly as one moves west. In Hokkaido, natto is sometimes served with squid ink for a dramatically colored variation. In parts of western Japan, where natto is less commonly eaten, preparations with okra or grated mountain yam are used to moderate the texture for those unused to it. Hikiwari natto \u2014 made from crushed or cracked soybeans rather than whole beans \u2014 has a finer texture and milder flavor, and is often preferred by those new to the food or those in regions where the full-bean variety is less culturally embedded.<\/p>\n\n\n\n Beyond flavor and texture, the fermentation of natto produces a nutritional profile that has drawn increasing scientific attention. In a fifty-gram serving, natto provides significant quantities of vitamin K \u2014 at 542% of the daily value, it is one of the richest dietary sources of this vitamin, particularly in the form of MK-7 (menaquinone-7), a form associated with bone and cardiovascular health. It is a rich source of iron (33% DV) and manganese (73% DV), and contains B vitamins, vitamin C, and complete protein from the soybeans themselves.<\/p>\n\n\n\n The fermentation also produces nattokinase \u2014 an enzyme that acts as a fibrinolytic agent, meaning it breaks down fibrin, a protein involved in blood clotting. Nattokinase has been studied for its potential cardiovascular benefits, and while clinical evidence remains developing, its presence in natto is one reason the food has attracted interest beyond Japan as global awareness of fermented foods and their health effects has grown.<\/p>\n\n\n\n None of this nutritional analysis was known to the soldiers who first encountered the transformed beans in their rice straw bundles, or to the Edo street vendors who sold fresh wara natto each morning to the working people of the city. They knew, through practice and experience, that natto was sustaining \u2014 that it kept well through winter, that it worked with the simplest of accompaniments, that a bowl of rice and natto was enough. The science of what the fermentation produces has arrived considerably later than the knowledge of what it does.<\/p>\n\n\n\n The most common preparation is the simplest: the plastic film is peeled back, the mustard and soy sauce sachets included in most commercial packages are added, and the natto is stirred \u2014 vigorously, with chopsticks \u2014 until the threads multiply and the mixture becomes glossy and cohesive. It is then poured over hot white rice and eaten immediately. The heat of the rice softens the natto slightly and amplifies the aroma. The contrast of the earthiness of the natto, the sweetness of the rice, and the sharp cut of mustard is the fundamental taste of natto as most Japanese people experience it.<\/p>\n\n\n\n Beyond this baseline preparation, natto appears in miso soup (natto-jiru, a preparation with ancient precedent), over soba noodles, in onigiri fillings, mixed with grated daikon and soy sauce in a preparation called soboro natto that is a specialty of Ibaraki. It can be dried and fried for a crunchy snack form, or aged with rice koji and salt to produce yukiwari natto \u2014 a fermentation within a fermentation, in which the already-fermented beans undergo a second transformation into something drier and more deeply savory.<\/p>\n\n\n\n Natto, in other words, is not a single food. It is a fermentation with a range of expressions, some ancient and some recent, each shaped by the hands and the traditions of the people who make it. At its core, however, it is always the same thing: a bacterium, a bean, warmth, and time. The simplest of fermentations, producing one of the most complex foods in the Japanese pantry.<\/p>\n\n\n\nThe Bacterium That Makes It Possible<\/h2>\n\n\n\n
Rice Straw and the Accidental Discovery<\/h2>\n\n\n\n
The Transformation of Production: From Straw to Science<\/h2>\n\n\n\n
Two Kinds of Natto: A Fermentation Before Natto<\/h2>\n\n\n\n
Regional Voices<\/h2>\n\n\n\n
What the Fermentation Produces<\/h2>\n\n\n\n
Eating Natto<\/h2>\n\n\n\n