Knowledge Base

Natto

Legume ferment · Traditional · peer-reviewed

Sticky, stringy fermented soybeans from a single bacterium — Bacillus subtilis var. natto — incubated hot and fast into Japan's breakfast classic.

Moderate to make
1 day ferment
protein, vitamin-k2, live-cultures supplied

Ingredients

  • Dry soybeans250 g
  • Natto starter (Bacillus subtilis var. natto)1 packet

How to make it

  1. Step 1

    Soak soybeans overnight, then pressure-cook or boil until very soft (softer than for tempeh).

  2. Step 2

    Drain thoroughly and cool to about 40–45 °C — warm enough for Bacillus, not scalding.

  3. Step 3

    Dust with natto starter and mix so every bean is coated.

  4. Step 4

    Spread in a shallow, covered tray or perforated container about 2–3 cm deep.

  5. Step 5

    Incubate at 40–42 °C for 22–24 h. A yogurt maker or warm oven works well.

  6. Step 6

    Done when beans are coated in sticky white film and pull long strings when stirred. Chill 24 h to develop flavour, then refrigerate.

What it is

Natto is whole soybeans fermented by Bacillus subtilis var. natto, a heat-loving bacterium. Unlike tempeh (a mould cake) or miso (a salted koji paste), natto is a short, hot, aerobic bacterial ferment. Finished beans are coated in a viscous, stringy polymer, smell strongly of ammonia and earth, and are traditionally eaten over rice with mustard and soy sauce.

The science

B. subtilis var. natto secretes enzymes that partially digest soy protein and produces poly-γ-glutamic acid (γ-PGA), the sticky threads that define good natto (Nishito et al., 2010). The same culture is associated with nattokinase, a fibrinolytic enzyme studied for cardiovascular effects, and with elevated menaquinone-7 (vitamin K2) levels in the finished beans (Sumi et al., 1987; Schurgers et al., 2007). Incubation near 40–42 °C for about a day selects for Bacillus and drives the characteristic texture and aroma.

Safety

Start from a commercial natto spore packet (or a spoon of fresh commercial natto) and use beans cooked thoroughly so competing microbes are reduced. Incubate hot and aerated. A strong ammonia smell is normal; discard if you see fuzzy coloured mould, pink slime, or a putrid (not ammoniacal) odour. Always refrigerate after the ferment.

Signs it worked / troubleshooting

  • ✅ Good: white sticky film, long strings when stirred, sharp ammonia-earth smell.
  • ⚠️ Dry or not sticky = too cool, too dry, or weak starter → hold nearer 41 °C, keep humidity up, use fresh spores.
  • 🚫 Coloured mould or rotten (non-ammonia) smell = contamination → discard.

How to store

Refrigerate promptly; natto keeps about a week cold, or freeze in portions. Flavour mellows after a day in the fridge — many makers prefer that "aged" day before eating.

References

  • Sumi H, Hamada H, Tsushima H, Mihara H, Muraki H (1987). A novel fibrinolytic enzyme (nattokinase) in the vegetable cheese Natto; a typical and popular soybean food in the Japanese diet. Experientia 43(10):1110–1111. doi:10.1007/BF01956052
  • Nishito Y, et al. (2010). Whole genome assembly of a natto production strain Bacillus subtilis natto from very short sequence reads. DNA Research 17(3):155–166. doi:10.1093/dnares/dsq009
  • Schurgers LJ, Teunissen KJ, Hamulyák K, et al. (2007). Vitamin K-containing dietary supplements: comparison of synthetic vitamin K1 and natto-derived menaquinone-7. Blood 109(8):3279–3283. doi:10.1182/blood-2006-08-040709

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