Natto Guide: What It Is, How to Eat It, and Why Japan Is Obsessed

Natto (納豆) is soybeans fermented by Bacillus subtilis natto — a bacterium that produces enzymes breaking down soybean proteins and fats while creating a characteristic sticky, mucilaginous coating on each bean. The result: dark brown soybeans with a complex savory-bitter flavor, a very strong ammonia-like smell, and strings of white mucilage that stretch between chopsticks.

Approximately 40–50% of Japanese people eat natto regularly. A significant proportion of Japanese people dislike it. For most non-Japanese first-timers, it is genuinely challenging. This guide explains what you're encountering and how to navigate it.

The Fermentation: What Natto Actually Is

The bacterium: Bacillus subtilis var. natto is a naturally occurring soil bacterium found throughout Japan. Traditional natto production involves wrapping soybeans in rice straw (wara, 藁) — which naturally harbors the bacteria. The classic fermenting technique is:

Soybeans are soaked, boiled until soft
Wrapped in rice straw
Left at approximately 40°C (rice straw insulates and provides ambient bacteria)
Fermented 24–48 hours

Modern commercial production:

Cooked soybeans are inoculated with pure B. subtilis natto culture
Placed in individual-portion polystyrene containers
Fermented in temperature-controlled chambers at 37–40°C for 16–24 hours
Refrigerated; the flavor continues developing during storage

What the fermentation produces:

Polyglutamic acid: The sticky substance coating the beans — a polymer of glutamic acid (the same amino acid that produces umami) that creates the characteristic stringy texture
Pyrazines: Compounds responsible for much of natto's distinctive smell and flavor
Nattokinase: An enzyme with documented fibrinolytic (blood clot-dissolving) properties
Vitamin K2 (menaquinone-7): Natto is among the richest food sources of MK-7, a form of vitamin K2 associated with bone and cardiovascular health

Why Natto Smells the Way It Does

The smell comes from two sources:

Ammonia: B. subtilis breaks down soybean proteins, producing ammonia as a byproduct — the same reaction that produces the smell of aged cheese. Stronger-smelling natto = more mature fermentation.
Pyrazines: Organic compounds with roasted, earthy, slightly ammonia-adjacent notes

The smell is strongest immediately after opening. Once natto is mixed and combined with soy sauce and mustard, the aromatic profile changes — the mixing introduces air, and the condiments moderate the sharp ammonia note. Many people who find the smell challenging find the taste much more manageable once it's seasoned and on rice.

How to Eat Natto

The Standard Method

What comes in the package: A standard commercial natto package (typically 40–45g per compartment, sold in sets of 3) includes:

The natto itself in a small polystyrene tray
A small packet of tare (soy sauce-based seasoning sauce)
A small packet of karashi (Japanese mustard)

The mixing step: Open the container, add the tare and mustard, and mix vigorously with chopsticks. The mixing creates more strings (polyglutamic acid forms as more surfaces are exposed) and is functionally important — it develops the flavor and integrates the seasoning. Count your stirs: dedicated natto enthusiasts mix 30–50 times (some claim 100+ times) to develop maximum string and flavor.

Serving: Spoon over hot rice (natto gohan, 納豆ご飯). The heat of the rice further modifies the texture and integrates the strings.

Additional toppings:

Raw egg yolk: enriches, mellows the flavor
Chopped green onion (negi): fresh contrast
Diced raw daikon: lightens the texture
Kimchi: adds acidity and heat (a popular modern combination)
Perilla (shiso): herbal brightness
Ponzu: more acidic than tare, lighter result

Natto in Cooking

Beyond the standard bowl preparation:

Natto maki (納豆巻き): Thin sushi roll with natto as the filling — a standard sushi restaurant item in Japan
Natto pasta: Natto, green onion, and soy butter sauce over spaghetti — a Japanese home cooking fusion
Natto soup (natto jiru): Natto dissolved into miso soup — produces a thicker, creamier texture
Natto toast: Natto on toast with cheese and sometimes kimchi — popular as a quick breakfast
Natto in okonomiyaki or pizza: Modern uses; the strings make it visually distinctive

Regional Natto Types

Kanto (East Japan) vs Kansai (West Japan): The strongest regional divide in natto consumption: natto is deeply embedded in Kanto food culture (Tokyo, Ibaraki, etc.) but significantly less popular in Kansai (Osaka, Kyoto, Kobe), where the miso-based food culture historically didn't embrace fermented soybeans in this form. Ibaraki Prefecture produces approximately 40% of Japan's commercial natto.

By bean size:

Regular (futsuu no natto, 普通の納豆): Standard soybean size; the most common
Small (kotsubu natto, 小粒納豆): Smaller beans; slightly different texture; preferred by some for easier eating
Extra small (okara natto, 超小粒): Very small beans; milder flavor
Hikiwari natto (挽き割り納豆): Soybeans crushed and fermented before packaging; less stringy, milder, easier for beginners — the suggested starting point for non-natto eaters

Wara natto (藁納豆): Traditional straw-wrapped natto (as opposed to polystyrene container); more complex flavor from the natural bacterial ecology of the straw; available in specialty shops and as a premium product. The Mito area (Ibaraki) is particularly associated with wara natto.

The Health Claims: What Is and Isn't Supported

Well-documented:

Nattokinase: The fibrinolytic enzyme isolated from natto has demonstrated ability to dissolve fibrin (blood clot material) in laboratory and some clinical studies. Important caveat: nattokinase is largely deactivated by stomach acid; the clinical picture is complex; it should not be treated as a pharmaceutical intervention.
Vitamin K2 (MK-7): Natto is exceptionally high in MK-7; 40g of natto can contain 200–400 micrograms of MK-7 (far exceeding typical daily requirements). MK-7 has demonstrated roles in bone mineral density and cardiovascular health. Note: individuals taking anticoagulants (warfarin/coumadin) should avoid natto — the K2 directly interferes with anticoagulant therapy.
Probiotic bacteria: B. subtilis natto survives stomach transit in some studies; whether it colonizes the gut is less clear than for Lactobacillus-type probiotics in fermented dairy.
Protein content: 40g of natto provides approximately 6-7g of protein; a complete protein with all essential amino acids.

Less certain: Many commercial nattokinase supplements claim cardiovascular benefits — the evidence base for supplements vs. actual natto consumption differs; cooking natto (heat) can deactivate some enzymes.

Starting to Eat Natto: A Realistic Approach

If you're new to natto and want to try it:

Start with hikiwari (挽き割り): The crushed type has less stringiness and a milder flavor — a more accessible entry point
Use plenty of soy sauce and mustard: The seasoning is not optional decoration; it genuinely changes the flavor profile
Eat with very hot rice: Hot rice integrates the texture better than room-temperature rice
Add a raw egg yolk: Fat from the yolk rounds the flavor significantly
Don't smell it first: Smell it after it's been seasoned and mixed; the raw smell is the most challenging part

The smell fades significantly as you become accustomed to it — most people who become natto eaters report that the smell that initially repelled them becomes a neutral or pleasant part of the experience over time. This is sensory adaptation, not forced tolerance.

Natto occupies a specific cultural position in Japan — it is simultaneously a humble daily breakfast food (cheap, quick, nutritious), a marker of regional identity (Kanto vs Kansai), an internet meme (the natto taste test for foreigners), and a serious health food. Understanding all of those layers makes the experience of eating it more legible. It is not a challenge to be conquered; it is a fermented food that Japan developed over approximately 1,000 years and integrated into one of the most longevous food cultures in the world.

The full recipes live in the book.

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