What is The Difference Between Natto and Miso

Both Natto and Miso are made from the same main ingredient, soya beans, and they are both fermented food products but that is where the similarities stop.

Short fermentation time  < 24 hoursLong fermentation time (months to years)
Bacterial cultureMold culture
Temperature range  38-42 degrees CelsiusTemperature range 15–25 degrees Celsius
Whole beansMashed beans
Contains only soya beansMay contain other ingredients
No added saltHighly salted
No umami flavorHas umami flavor
Aerobic fermentationAerobic and Anaerobic fermentation
Traditionally a breakfast mealTraditionally made into soup

Short fermentation time vs long fermentation time

Natto is made in less than a day

The beans are soaked for 3-5 hours until they are doubled in size then they are streamed or cooked in a presser cooker until they can be squished between two fingers.  Once they are cooked they are inoculated with a starter and incubated anywhere between 16-20 hours.

Once the fermentation time is over the beans can be refrigerated, frozen or eaten immediately although the flavor is better once it has aged 48-92 hours.

Miso can be made in a week to several years

When making miso it takes three days just to start the fermentation process.  The soya beans and rice or barley are inoculated in a controlled environment before they are mashed together and placed into aging tanks where they remain for at least a week to several years depending on the type of miso being made.

Yeast culture vs Mold culture

There is just one culture used to produce Natto

Natto is fermented with Bacillus subtilis which is a yeast culture which propagates through spores.  It is commonly found on grass especially straw. Natto used to be made by wraping hot steamed soybeans in straw and waiting a day. It is now made by using some finished natto as a starter or from spores of Bacillus subtilis.

There are several types of microorganisms which are required for the production of miso.

The first is Aspergillus oryzae, which is a mold used to produce the enzymes needed to convert the starches in the rice, barley or bean starter into sugars. Once Aspergillus oryzae has produced enough of these enzymes it is called koji. At this point the koji is mixed with the miso mash and a high amount of salt which slows or stops the action of Aspergillus oryzae. At this point lactic acid bacteria and the salt tolerent yeast Zygosaccharomyces rouxii take over the fermentation using the sugars produced by the enzymes from the koji for energy.

Warm temperature vs cooler temperature

Natto is fermented above normal room temperature in the range of 37-53 degrees Celsius.  For best results maintaining a temperature of 40-50 degrees Celsius is ideal.  This provides an environment for the culture to grow rapidly and dominate its environment giving little chance for pathogenic bacterial cultures to grow.

Miso fermentation is a multi-step process with varying temperatures which mimic the atmospheric temperature of the traditional fermentation time.

The first step is to make koji which needs a temperature of 28-38 degrees Celsius.

Next the koji is mixed with steamed rice and soya beans and fermented at about 10 degrees Celsius where it ages for a varying period of time depending on the type of miso.  Traditionally the miso would be kept in open air locations so as the ambient temperature fluctuated through the seasons the miso fermentation temperature would also fluctuate.

Whole beans vs mashed beans

The preparation of the beans for both natto and miso is basically the same.

  • Soak the beans until they are double in size from the dried beans.
  • Steam or boil the beans until they are soft enough to squish between two fingers.

They begin to vary when the beans are inoculated with the starter culture.  For natto the beans are left whole and the bacillus subtilis has to penetrate the bean structure to find its energy.  This is why natto made with small beans is preferred to natto made with larger beans.  The bacterial culture has more surface area to grow on while the space between the beans allows adequate oxygen for the bacteria to multiply quickly.

If the beans were mashed the available surface area would be only the edge which is exposed to the air.  This would slow the fermentation down considerably and allow other cultures to take hold and grow.

Miso is made by mashing the beans and adding the culture to the mashed beans.  This provides the koji adequate contact with its food source to grow rapidly and dominate the culture.  Once the fermentation is complete the miso is a paste which is added to other dishes as a flavoring or condiment.

Contains only soya beans vs contains other ingredients

Natto is made with only soya beans with no added ingredients.  Although the bacterial culture which is used to make natto is also used to ferment other types of beans or seeds the resulting fermentation is not called natto.

Miso is made with a variety of ingredients depending on the type of miso being made.

Some popular miso types and thier base ingredients

Miso nameingredients
Shiro Miso or White misoSoya beans and rice
Shinshu Miso or yellow misoSoya beans and rice
Aka Miso or red misoSoya beans and rice
Mugi Miso or barley misoSoya beans and barley
Hatcho Miso or Mame MisoSoya beans only

Miso contains rice flour which is used to spread the culture evenly throughout the bean mash.  The technique for evenly mixing the koji into the mash is to inoculate some steamed rice with the culture and let it grow until it sporalates.

Once this happens the rice flour is mixed in and sifted out.  This will attach the culture to the rice flour which is then mixed in with the miso mash.

No added salt vs Added salt

Salt is usually used in fermentation recipes to prevent unwanted bacterial growth.  Such fermentations like sauerkraut, fermented vegetables and kimchi all use salt as a preservative while the intended bacterial culture grows.

Miso uses salt in a high percentage.  This is because of its long fermentation time with varying temperatures.  The salt inhibits the growth of unwanted molds which can give the miso an off flavor. 

Natto is a fast ferment and does not require added salt to prevent spoilage.  The culture Bacillus subtilis grows quickly when put into the proper growing environment preventing the growth of unwanted cultures.

Aerobic vs Aerobic and Anaerobic

Natto is an aerobic fermentation which means the bacterial culture which turns soya beans into natto need the presents of oxygen to grow.

The original method of making natto is to wrap the cooked soya beans in straw and store in a warm place for 24 hours or so.  No starter culture was added as the bacterial culture which makes natto is prevalent in nature, especially on straw and other grasses. The culture would grow rapidly in the presents of oxygen and insulated from the straw.

To make miso is a multi-step process which includes the culturing of koji, which is an aerobic process.  Rice is inoculated after it has been soaked and steamed and then fermented for up to 3 days.  The koji is then used to inoculate the rice and soya bean mash.  It is then packed into aging containers and sealed tightly to prevent access to oxygen.

Nutrient differences

Although Natto and Miso are both made from soya beans the nutrient content is vastly different.  In some cases Miso has a nutrient which Natto doesn’t such as Beta Catotene and in other cases Natto has a nutrient which Miso doesn’t such as Vitamin C.

They both contain the same amount of fiber at 19% of the daily value but vary widely in other cases such as the presents of iron makes up only 14% of the daily value whereas natto contains 48%.

To complicate the issue you need to take into account the normal serving sizes of miso and natto.  Miso is usually eaten as a condiment or in Miso soup and a serving of a tablespoon would be typical.  A tablespoon of miso weights approximately 17 grams well below the calculated 100 gram values below.

Natto is sold in 40-50 gram packages which is then added to rice for breakfast.

All calculations below are for 100 g serving size.

Nutrient Amount Unit DV Amount Unit DV
Alanine0.5 G 0.798 G 
Arginine0.784 G 0.909 G 
Ash12.81 G 1.9 G 
Aspartic acid1.171 G 1.956 G 
Calcium, Ca57 MG4%217 MG17%
Calories198 KCAL 211 KCAL 
Carbohydrate25.37 G9%12.68 G5%
Carotene, beta52 UG 0 UG 
Choline72.2 MG 57 MG 
Copper, Cu0.42 MG47%0.667 MG74%
Cystine0 G 0.22 G 
Docosanoic acid0.05 G 0 G 
Eicosenoic acid0.025 G 0 G 
Fat6.01 G8%11 G14%
Fiber5.4 G19%5.4 G19%
Folate19 UG 8 UG 
Folate, DFE19 UG5%8 UG2%
Folate, food19 UG 8 UG 
Fructose6 G 0G 
Glutamic acid1.915 G 3.337 G 
Glycine0.447 G 0.646 G 
Heptadecanoic acid0.01 G 1.168 G 
Heptadecenoic acid0.03 G 0G 
Hexadecanoic acid0.75 G 0 G 
Hexadecenoic acid0 G 0.031 G 
Histidine0.243 G35%0.512 G73%
Iron, Fe2.49 MG14%8.6 MG48%
Isoleucine0.508 G36%0.931 G67%
Leucine0.82 G30%1.509 G55%
Lysine0.478 G23%1.145 G55%
Magnesium, Mg48 MG12%115 MG29%
Maltose0.2 G 0 G 
Manganese, Mn0.859 MG37%1.528 MG66%
Methionine0.129 G 0.208 G 
Methionine + Cysteine0.129 G12%0.208 G20%
Monounsaturated fatty acids1.118 G 2.43 G 
Niacin0.906 MG6%0 MG0%
Octadecadienoic acid2.479 G 5.476 G 
Octadecanoic acid0.2 G 0.393 G 
Octadecatrienoic acid0.405 G 0.734 G 
Octadecenoic acid1.043 G 2.399 G 
Pantothenic acid0.337 MG7%0.215 MG4%
Pentadecenoic acid0.02 G 0 G 
Phenylalanine0.486 G 0.941 G 
Phenylalanine + Tyrosine0.838 G48%1.497 G86%
Phosphorus, P159 MG23%174 MG25%
Polyunsaturated fatty acids2.884 G 6.21 G 
Potassium, K210 MG4%729 MG16%
Proline0.619 G 1.403 G 
Protein12.79 G26%19.4 G39%
Riboflavin0.233 MG18%0.19 MG15%
Saturated fatty acids1.025 G5%1.591 G8%
Selenium, Se7 UG13%8.8 UG16%
Serine0.601 G 1.121 G 
Sodium, Na3728 MG162%7 MG0%
Sugars6.2 G 4.89 G 
Tetracosanoic acid0 G 0.031 G 
Tetradecanoic acid0.015 G 0 G 
Thiamin0.098 MG8%0.16 MG13%
Threonine0.479 G46%0.813 G77%
Tocopherol, alpha0.01 MG 0.01 MG 
Tryptophan0.155 G55%0.223 G80%
Tyrosine0.352 G 0.556 G 
Valine0.547 G30%1.018 G56%
Vitamin A87 IU2%0 IU0%
Vitamin A, RAE4 UG 0 UG 
Vitamin B120.08 UG3%0 UG0%
Vitamin B60.199 MG15%0.13 MG10%
Vitamin C0 MG0%13 MG14%
Vitamin E0.01 MG0%0.01 MG0%
Vitamin K29.3 UG24%23.1 UG19%
Water43.02 G 55.02 G 
Zinc, Zn2.56 MG23%3.03 MG28%

Traditionally a breakfast meal vs Made into soup

The traditional Japanese use for natto is as a breakfast meal.  Made up of warm rice, natto, soya sauce and chives.

Miso is used traditionally to make miso soup, used in sauces or as a condiment for main course meals.

Michael Grant

Mike has been an enthusiast of fermentation for over ten years. With humble beginnings of making kombucha for himself to the intricacies of making miso, vinegar and kefir. He makes a wide variety of fermented foods and drinks for his own consumption and family and friends. Being a serial learner he began experimenting with a wide variety of fermented products and learning widely from books, online from content and scientific studies about fermentation, its health benefits, how to use fermented food products in everyday life and the various techniques used to produce them both traditionally and commercially. With a focus on producing his own fermented products in an urban environment with little access to garden space he began Urban Fermentation to help others who want to get the benefits of fermentation in their lives. He provides a wide variety of content covering fermented drinks like kombucha and water kefir, milk kefir and yogurt, vinegar production and lacto-fermentation such as pickles, sauerkraut for those who have to rely on others for food production. With an insatiable hunger to know more about fermentation from all nations and cultures he also has learned to make natto, miso and soy sauce, with more to come as the body of knowledge about fermentation is constantly expanding and becoming more popular as time passes.

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