KO EN Japanese Side dish⏱ 90 minEdit history

Natto (Soybeans Fermented with Bacillus subtilis)

Name: Natto (Soybeans Fermented with Bacillus subtilis)
Prep time: 30 min
Cook time: 1 h
Total time: 1 h 30 min
Yield: 6 servings
Cuisine: Japanese
Ingredients: 300 g dried soybeans; 2 L water; 1 pinch natto spores; 2 tbsp boiled and cooled water; 1 tsp soy sauce; 0.5 tsp karashi mustard; 1 spring onion; 1 egg yolk; 1 bowl hot rice

Japan’s fermented soybeans: boiled beans inoculated with Bacillus subtilis natto and held at 40°C for a day. This site’s fermentation guide lists natto almost exactly, under failures — slimy and stringy, no salt at all, deliberately warm, and air let in rather than kept out. The guide’s thesis is that the safety of a ferment comes not from cleanliness but from the acidity dropping fast. Natto’s pH climbs to about 8, and its safety comes from a pure culture on sterilised beans: from cleanliness, exactly.

Ingredients

6servings

The beans
dried soybeans · small beans suit natto better300 g
water · for soaking2 L
Starter
natto spores · powdered starter; a tablespoon of shop natto will do instead1 pinch
boiled and cooled water · to disperse the starter2 tbsp
To serve
soy sauce1 tsp
karashi mustard0.5 tsp
spring onion1
egg yolk · for natto tamago kake gohan1
hot rice1 bowl

Steps

Soak the beans overnight. They should swell to nearly three times their size.
Change the water and boil them very soft — a bean should crush with no resistance between your fingers. Thirty to forty minutes in a pressure cooker, three or four hours in a pot.
⏲ 40 min
Scald the container and spoon with boiling water. Unlike every other ferment here, cleanliness is the safety mechanism: there is no salt and no acid to hold anything back, and the only defence is a pure culture taking the beans first.
⏲ 10 min
Drain the beans and, while they are still hot, sprinkle over the dispersed starter and mix. Hot beans kill off what survived the boil, while the natto spores ride it out.
⏲ 5 min
Spread them in a shallow dish no more than 2cm deep, cover with film and pierce it in several places. Bacillus subtilis needs oxygen to grow, which is the exact opposite of the usual instruction (fermentation basics).
⏲ 5 min
Hold at 40°C for 20-24 hours — a yogurt maker, an oven proving setting or a heat mat all work. Below 30°C other microbes win; above 50°C the natto bacteria die too.
It is done when the surface is filmed over white, it pulls into threads when stirred, and it smells faintly of ammonia. Rest it overnight in the fridge, which settles the smell and lengthens the threads.
Stir it hard before the soy sauce goes in, not after. The more you stir the longer the threads; soy sauce added first thins it and shortens them. Top with mustard and spring onion and spoon it over hot rice.
⏲ 2 min

Tips & Variations

Variations

Natto tamago kake gohan: natto and a raw egg yolk over hot rice — the commonest breakfast form.
Natto maki, natto soba, natto fried rice: rolled in nori, over buckwheat noodles, stirred into fried rice.
Hikiwari natto: made from beans crushed before fermenting. No skins, softer, finer threads.
Cheonggukjang: the same bacterium, a different product. That one ferments two or three days on rice straw with wild flora, then gets salted and mashed into a paste for stew. Natto uses a pure starter, finishes in a day, and is eaten as it is.
If the smell is daunting: never skip the overnight rest in the fridge, be generous with mustard and spring onion, and wrap it in nori, which mutes it considerably.

Tips

Fermentation basics' failure list is a description of success here. That guide says "Slimy, with a rotten smell → failed" and "Brine gone thick and stringy → wrong microbes. Discard." Natto aims at precisely that state.
All three of its levers run backwards. No salt at all, against the guide's 2-3%; 40°C deliberately, rather than 20-25°C; and air let in through pierced film rather than kept out, because Bacillus subtilis is aerobic and will not grow without oxygen.
And the thesis itself inverts. The guide says "the safety of a ferment does not come from cleanliness — it comes from the acidity dropping fast." Natto makes ammonia rather than acid, so its pH climbs to about 8, and its safety comes from a scalded container and a pure culture: from cleanliness, exactly. That is the only reason a salt-free, acid-free ferment can sit at 40°C for a day.
Hongeo-hoe goes the same direction by a different road. That one also turns alkaline, but through urea in the flesh being converted by wild flora, over weeks in the cold. This is a pure culture, 40°C, one day.
The threads are poly-γ-glutamic acid, a polymer the bacterium secretes — literally glutamate linked into a chain (building umami). Cheonggukjang's famous threads are the same substance, and that page records that they appear without saying what they are.
Stirring makes the threads. The polymer aligns as you work it, which is why the advice to stir a hundred times is not entirely a joke.
Boiling the beans soft is half the recipe. The bacteria only grow on the surface of a bean, so an underdone, firm bean stays unfermented in the middle.