Natto: History and Origins

Natto was almost certainly never invented — it was discovered, and probably more than once, by accident. Somewhere in early Japan, boiled soybeans wrapped in rice straw met the wild Bacillus subtilis living on that straw, sat warm for a day or two, and emerged sticky, pungent, and oddly nourishing. This article traces what the historical record actually supports: the Chinese fermented-soybean foods that came before it, the famous battlefield and temple legends that Japanese tradition tells about its origin (named here as legends), the etymology that ties its name to monastery kitchens, the first firm written mention in a Kyoto noble's diary of 1405, the early-twentieth-century science that replaced rice straw with a pure starter culture, and one genuinely datable modern discovery — the 1980 identification of the enzyme nattokinase. Where the record is solid we say so; where a claim is folklore or still uncertain, we mark it plainly.

Table of Contents

  1. A Food Born of the Soybean and the East-Asian Ferment
  2. The Battlefield and Temple Legends
  3. What the Name Means: Natto and the Temple Kitchen
  4. Into the Written Record: The Diary of 1405
  5. Rice Straw, Wild Bacteria, and the Old Way of Making It
  6. From Straw to Starter Culture: The Modern Bacillus
  7. A Regional Food Becomes a National Breakfast
  8. A Real Discovery: Nattokinase (1980)
  9. Research Papers and References
  10. Connections
  11. Featured Videos

A Food Born of the Soybean and the East-Asian Ferment

Natto's story begins not with a person but with two older things: the soybean, and East Asia's long habit of fermenting it. The soybean (Glycine max) was domesticated in East Asia — the genetic and archaeological evidence points to the region of China and surrounding East Asia thousands of years ago — and from it grew an entire family of fermented foods: soy sauce, miso, tempeh, and the salty fermented soybeans the Chinese call douchi. Natto belongs to this family. It is a Japanese member of a much wider East-Asian tradition of letting microbes transform the humble soybean into something more digestible, more savoury, and longer-keeping.

The most likely ancestor of natto is a salty, mould-fermented soybean food brought from China. A product of this kind — later known in Japan as shiokara nattō ("salty natto"), made with Aspergillus moulds rather than Bacillus bacteria — was associated with Buddhist temple cooking and is documented in Japan well before the sticky, stringy natto most people picture today. The familiar modern food, technically itohiki nattō ("stringy natto"), is the bacterial one: it is fermented by Bacillus subtilis var. natto, develops long sticky threads, and uses no salt during fermentation. One widely repeated idea is that this saltless, bacterial natto may have emerged partly because salt was scarce and precious in early Japan, nudging soybean ferments toward a salt-free path. That is a reasonable historical interpretation rather than a proven sequence of events, and this page treats it as such.

What is firm is the lineage: natto sits downstream of China's ancient soybean ferments, arrived in Japan within that current, and then became something distinctively Japanese. The two key facts to carry forward are that natto's earliest relatives were salty temple foods, and that the version the world now knows is a separate, bacterial, sticky descendant.

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The Battlefield and Temple Legends

Japan tells two favourite stories about how natto was first discovered. Both are legends — widely repeated, charming, and almost certainly not literal history — and both turn on the same accidental mechanism: boiled soybeans left wrapped in rice straw long enough to ferment on their own.

The most popular legend attaches to the eleventh-century warrior Minamoto no Yoshiie (1039–1106) and the northern campaigns of his era (the conflicts of the 1080s, in the period of the Gosannen War). In the usual telling, his soldiers were boiling soybeans to feed their horses when they were suddenly attacked; they hurriedly bundled the hot beans into rice-straw bags, carried them for a day or two on horseback, and on opening the bundles later found the beans had fermented into something sticky that turned out to be good to eat. The straw, we now know, would indeed have carried the wild Bacillus needed to start the ferment, and the warmth of travel would have kept it going — so the story is at least biologically plausible, even if there is no contemporary record proving it happened.

A second legend reaches further back, to Prince Shōtoku (574–622), the early statesman associated with the spread of Buddhism in Japan; in this version he wraps leftover boiled soybeans in straw — in some tellings, to feed his horse — and accidentally produces natto. Like the Yoshiie story, it is a tale of origin rather than a documented event. The honest reading of both legends is the same: they capture a real truth about how natto is made — soybeans plus straw plus warmth — while assigning that discovery to a famous name, which is how folk traditions everywhere tend to explain the origins of an old food. No single person invented natto.

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What the Name Means: Natto and the Temple Kitchen

The word natto is written with two Chinese characters, 納豆, meaning roughly "stored / offered beans." The most widely cited explanation of the name ties it to Buddhist temples. A temple complex traditionally had an office or storehouse called the nassho (納所) — a place connected with receiving offerings and with the temple kitchen — and this is said to be where monks made and kept fermented soybeans. The food became, in effect, "the bean stuff from the nassho," rendered in characters as 納豆 and read nattō. This temple-kitchen etymology is recorded in the Honchō Shokkan, a Japanese food treatise of 1695, which also gives one of the early written mentions of natto's supposed healing or strengthening effects.

Two cautions belong here. First, the temple-kitchen derivation, though the standard and best-supported account, is an etymology reconstructed from later sources rather than a fact recorded at the moment the word was coined; competing readings of the characters exist. Second, the word nattō in the oldest texts did not necessarily mean the sticky food we eat now. The term appears in the written record during the Heian period (794–1185) — it is generally traced to a mid-to-late-eleventh-century work, the Shin Sarugakuki — but there it most likely referred to the older salty temple-style natto, not to the stringy, bacterial itohiki nattō. The name, in other words, is older than the modern food it now names.

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Into the Written Record: The Diary of 1405

Legends aside, the first firm written reference specifically to the sticky, stringy natto we recognise today comes from a personal diary. In a diary entry of 1405, the Kyoto aristocrat Yamashina (Fujiwara) Noritoki recorded itohiki natto — the "stringy beans" — giving historians a concrete date by which the modern bacterial food clearly existed and was being eaten by the nobility. This 1405 mention is firm enough that the standard English-language history of the food, William Shurtleff and Akiko Aoyagi's History of Natto and Its Relatives, takes it as the starting point of its very title, which runs from 1405 to 2012.

After 1405, references multiply. The stringy food turns up again in a fifteenth-century text on vegetarian fare, and over the following centuries natto becomes a recognisable item of everyday Japanese food culture, eaten with rice and sold in its rice-straw wrapping. It is worth keeping the two thresholds distinct: the word natto is older and first attached to a salty product, while the firmly documented history of the sticky modern food begins in earnest with that 1405 diary. Everything before it — the battlefield and temple legends, the speculation that ancient straw-wrapped soybeans were fermenting in Japan far earlier — is plausible but not securely documented.

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Rice Straw, Wild Bacteria, and the Old Way of Making It

For most of natto's history the method was beautifully simple and depended on something farmers already had everywhere: rice straw. Boiled soybeans were packed into a bundle of straw and kept warm. The straw was not just a wrapper but the source of the culture: Bacillus subtilis lives naturally in soil and on rice straw as a heat-resistant spore, and when warm beans are sealed inside, those spores wake up, multiply, and ferment the beans. This straw-wrapped form, wara-nattō, is the traditional package in which natto was made and sold, and it is still produced as an artisanal style today.

The signature stickiness has a real biochemical explanation. As the bacterium grows it secretes long sticky polymers — chiefly poly-gamma-glutamic acid together with fructan sugars — and it is these that form the famous stretching threads (ito-hiki, "thread-pulling") when you stir natto. The pungent aroma comes from the same metabolic activity. None of this was understood for most of natto's history, of course; cooks simply knew that straw, warmth, and time reliably turned beans into natto. The reliability is the point: a method this forgiving and this dependent on a common material is exactly the kind that could have been discovered independently in many places, which is part of why pinning natto's origin to one event or person is impossible.

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From Straw to Starter Culture: The Modern Bacillus

The decisive modern change in how natto is made came in the early twentieth century, when Japanese science replaced wild straw fermentation with a controlled, pure culture. The figure usually credited is the bacteriologist Hanzawa Jun, who in the early 1900s worked on isolating the Bacillus subtilis responsible for natto so that producers could inoculate beans with a known starter rather than relying on whatever happened to be living on a given batch of straw. This shift — broadly placed in the Taishō period (1912–1926) — let makers ferment natto cleanly and consistently in any container, with steady quality and far less risk of spoilage or contamination.

It is from this work that the bacterium acquired the name most often used for it: Bacillus subtilis var. natto (in Japanese, nattō-kin) — the natto variety of a very common, well-studied soil bacterium. The practical consequence is the natto on supermarket shelves today: produced with purified starter cultures in temperature- and humidity-controlled rooms, packed in small foam or film containers rather than straw, and far more uniform than anything the old method could guarantee. The straw tradition did not vanish — wara-nattō survives as a prized artisanal product — but the everyday food became an industrial one. This is the cleanest example in natto's story of named scientists turning a folk craft into a reproducible process; it is a milestone of production, not the "invention" of the food, which long predates it.

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A Regional Food Becomes a National Breakfast

Natto has long carried a strong regional identity. It is most associated with eastern and northern Japan, and the city of Mito, in Ibaraki Prefecture, is famous as a natto heartland and markets itself as a home of the food. (Such "birthplace" claims are matters of local pride and culinary fame rather than of provable first-origin, and several regions have natto traditions.) Historically, natto was an inexpensive, protein-rich everyday food — sold fresh in its straw bundle, eaten with hot rice, and valued in folk tradition as warming and strengthening, a reputation echoed in that 1695 food treatise. These traditional health beliefs are reported here as part of the food's cultural history, not as medical claims.

Over the modern era natto spread from a regional speciality toward a national staple, helped by industrial pure-culture production, refrigeration, rail and road distribution, and convenient single-serving packaging with its little sachets of sauce and mustard. Today natto is a familiar Japanese breakfast item nationwide, eaten over rice with soy sauce, mustard, and green onion, and sometimes a raw egg — even as it remains, by reputation, one of Japan's most polarising foods for newcomers because of its smell, slime, and strong flavour. The arc is a common one in food history: a cheap, local, slightly humble ferment, sustained for centuries by ordinary households, becomes first an industrial product and then a point of national identity — and, lately, an object of international nutritional interest, the subject taken up in the final section.

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A Real Discovery: Nattokinase (1980)

Almost everything in natto's history is the slow, anonymous work of tradition — but one part has a real discoverer, a date, and a documented experiment. In 1980, the Japanese researcher Dr. Hiroyuki Sumi, who was studying clot-dissolving (fibrinolytic) enzymes, placed a small piece of natto onto an artificial blood clot in a laboratory dish and found that the clot dissolved over a number of hours. The enzyme responsible — a clot-busting protease that natto's bacterium produces during fermentation — was something he had not been looking for in a food at all, and he named it nattokinase.

The finding was formally published a few years later. In 1987, Sumi and colleagues reported it in the journal Experientia under the title "A novel fibrinolytic enzyme (nattokinase) in the vegetable cheese Natto; a typical and popular soybean food in the Japanese diet." That paper introduced the word nattokinase to science and launched decades of research into the enzyme as a potential cardiovascular supplement. It is important to mark exactly what was and was not discovered: the cooks of medieval Japan did not "discover" nattokinase, and natto itself has no inventor. What Sumi did was identify and name one specific molecule, produced by the very Bacillus subtilis that makes natto sticky, and show what it could do to a clot in a dish. Tradition supplied the food; modern enzymology gave one of its components a name and an address.

This is also where history hands off to the present. Whether the nattokinase in a bowl of natto, eaten and digested normally, produces meaningful effects in the body — as opposed to concentrated supplements taken in isolation — is a separate and still-debated scientific question, not a settled historical fact. The evidence, mechanisms, and cautions are covered on the companion Natto Benefits pages and on the main Natto page; this history is concerned only with how the food, and its one named enzyme, came to be.

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Research Papers and References

The list below pairs the key documented scientific milestone in natto's history with reputable food-history and review sources and curated PubMed topic searches. Historical primary texts (the diary of Yamashina Noritoki, 1405; the Honchō Shokkan, 1695) and the origin legends are named in the article as historical and folkloric sources, not as modern citations. Author names, titles, and journals are given as plain text; only the stable DOI, PMID, ISBN, or archive link is hyperlinked, and each opens in a new tab.

  1. Sumi H, Hamada H, Tsushima H, Mihara H, Muraki H. A novel fibrinolytic enzyme (nattokinase) in the vegetable cheese Natto; a typical and popular soybean food in the Japanese diet. Experientia. 1987;43(10):1110-1111. — doi:10.1007/BF01956052
  2. Shurtleff W, Aoyagi A. History of Natto and Its Relatives (1405-2012). Lafayette, CA: Soyinfo Center; 2012. — Soyinfo Center: History of Natto (1405-2012)
  3. Weng Y, Yao J, Sparks S, Wang KY. Nattokinase: an oral antithrombotic agent for the prevention of cardiovascular disease. International Journal of Molecular Sciences. 2017;18(3):523. — doi:10.3390/ijms18030523
  4. Hodgkin J. Nattō. In: Nippon.com — Fermented Friend or Foe: Unwinding the Tangled "Nattō" Threads. — Nippon.com: the tangled history of natto
  5. Natto (food). Encyclopaedia Britannica. — Britannica: Natto
  6. Natto history, fermentation, and Bacillus subtilis — PubMed: natto, Bacillus subtilis, and fermentation
  7. Nattokinase, fibrinolysis, and fermented soybean foods — PubMed: nattokinase and fibrinolytic activity

External Authoritative Resources

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Connections

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