It is the action of the natto bacillus that converts soybeans into natto through the process of fermentation. The natto bacillus which plays the leading role in fermentation is one of the members of a type of microorganism known as Bacillus subtilis. There are said to be around three million varieties of microorganisms in the world, of various types and with various properties. These include bacteria, fungi, protozoa, algae and so on. ("Basics of Fermentation" Hiroshi Tachi, Seibundo Shinkosha Publishing Co., Ltd.)

Bacillus subtilis is a type of bacteria. The subspecies that produces a natto-like aromatic fragrance and fine threads — the natto bacillus — is named Bacillus subtilis var. natto.

Bacteria of the Bacillus subtilis family are found everywhere: in soil, in the air and so on. In these ecosystems, they decompose animals and plants and return them to the soil and air.

Scientific name
Bacillus subtilis
Natto bacillus: Bacillus subtilis var. natto

"Decomposition" or breaking down is a key concept for the creation of natto.
The natto bacillus breaks down the proteins, lipids and other components of the soybean by secreting an enzyme of its own creation, and propagates as it incorporates these components. Vitamins, aromatic substances, fine threads and so on are produced as byproducts of the decomposition process. The components of the soybeans are also converted into a more easily digestible form.

The natto bacillus performs this series of actions as part of its own vital activities. We refer to this process as "fermentation" and are fortunate to receive its benefits.

This section covers some of the nutritious components produced in the course of soybean fermentation by the natto bacillus.
* The following information is based on the 2020 Standard Tables of Food Composition in Japan, 8th revision.

One of the symbols of natto is the viscous lines that extend from the beans and wrap themselves around eating implements. Japanese use terms such as "threads" and "thread-pulling" to describe these viscous substances.
However, most people probably do not know the substance making up these threads. They just have a vague sense that the viscosity of natto seems somehow healthy.

The viscous substances in natto — in other words, the thread components — actually comprise a complex tangle of γ-polyglutamate, to which are attached several thousand components of glutamine (a type of amino acid), and a polymer, to which are attached several levans (fructans) (a type of dietary fiber). The γ-polyglutamate is primarily what give the threads their viscosity, while the levans are said to stabilize the viscosity.

The γ-polyglutamate is produced from the glutamate that is created when the proteins in the soybeans are broken down by the natto bacillus. The levans are a product of the fructose which is produced when the sugars in the soybeans are broken down. The viscous substances in natto are produced by the natto bacillus using these components in the soybeans.

For what purpose does the natto bacillus create these viscous substances?
In a word: to protect itself.

The natto bacteria divide and propagate on the surface of the soybean. As long as there are few bacteria, however, no viscous substances are created. But when the bacteria propagate steadily and their density increases, they strive to store nutrients, out of concern for a time when the soybean will not provide sufficient food. (Naturally we cannot interview the natto bacillus, so terms such as "concern" and "strive" are used for illustrative purposes only.) The amino acids that are derived when the natto bacillus breaks down proteins are converted into γ-polyglutamate, and the bacteria are thought to envelop themselves in this substance.

The viscous substances are also able to hold moisture, preventing drying and acting as a barrier to protect the natto bacillus from viruses. In addition, the threads also apparently act to connect the bacteria to prevent them from being separated from one another. The viscous substances could be called an all-purpose safety net for the natto bacillus.

The viscous substances have a structure like that of a carpenter's folding ruler. They collapse into a folded state and then, when they are pulled, the fold lines stretch outward and the viscous substances expand. This is the mechanism by which the natto threads are able to stretch so far.

This has been an extended explanation of the viscous substances of Bacillus subtilis that make up the natto bacillus.
Finally, the vague impression that the viscosity of natto must be healthy turns out to be correct.
The γ-polyglutamate has been confirmed to promote the absorption of calcium in the intestine.
ja (jst.go.jp)

Polyamine is a substance synthesized from amino acids that are contained in the cells of all living things. It affects propagation and survival within the cell and is essential for living things — not only animals and plants but microorganisms as well.

Recent research into polyamine has reported that it has anti-aging properties. An increase in polyamine concentration in the blood has been shown to suppress the substances that trigger arteriosclerosis, one type of aging, and it also tends to suppress the chronic inflammation reaction of blood vessels.

Moreover, the effects of polyamine do not only relate to arteriosclerosis. It also helps to improve blood circulation and rejuvenate blood vessels and the cells of the immune system and so on. In addition, an increased quantity of polyamine in the body is thought to result in a constitution that can more easily burn fat, making it more difficult to gain weight.
"The polyamine in natto can prevent aging and arteriosclerosis!" (PDF file)

Polyamine can be synthesized in the body. Unfortunately, the amount of polyamine in the body is known to decrease as one ages.
However, it is possible to ingest polyamine from foods, and moreover it is easily absorbed from the stomach and large intestine. Happily, it is possible to maintain a high concentration of polyamine in the blood by eating foods that contain large quantities of polyamine.

At this point, we come back finally to natto. As you will see, natto contains large quantities of polyamine. Data have shown that a one-person serving package of natto contains 1/5 of the recommended daily intake of polyamine for a Japanese person. "What is the relationship between polyamine and natto? Includes major functions and recipes using natto — Health information column" (Suntory-Kenko.com)

Originally known to promote digestion, natto also enables one to ingest its polyamine content. For people concerned about anti-aging, this makes natto doubly delicious.

Natto bacillus: A key player in maintaining a healthy gut

Dietary fibers have been recognized as active ingredients that maintain the good condition of the stomach. They have been defined as "an aggregate of indigestible components in food that are not digested by people's digestive enzymes." Dietary fibers comprise a diverse array of components with various textures, some of which do and some of which do not dissolve in water.
Dietary fibers increase stool quantity and have been shown to be used by intestinal bacteria to regulate the environment in the large intestine, and even to increase the quantity of these bacteria.

The "Dietary Intake Standards for Japanese (2020 edition) " established by the Ministry of Health, Labor and Welfare set a recommended daily allowance (the quantity that should be ingested by modern Japanese as a near-term objective to prevent lifestyle-related diseases) of at least 21g and 18g of dietary fibers for men and women, respectively, between the ages of 18 and 64.
However, the quantity consumed by Japanese has been declining. In the most recent report, the average daily intake was estimated to be around 14g.
Need for dietary fibers and health / e-HealthNet (Ministry of Health, Labor and Welfare) (mhlw.go.jp)

Natto contains 6.7g of dietary fibers per 100g. As one individual serving package of natto contains around 45g, this works out to more than 3g of dietary fibers consumed per meal.

Incidentally, using the same per-100g measure to compare foods that are thought to contain large quantities of dietary fibers, konyaku slab contains 2.2g, raw sweet potato also contains 2.2g, raw cabbage contains 1.8g, and raw maitake mushrooms contain 3.5g. Boiled soybeans contain 8.5g, a higher dietary fiber content than natto, but it should be remembered that natto is more easily digestible than soybeans.

The natto bacillus secretes various enzymes to break down the nutrients in soybeans. These include protease, which breaks down proteins into amino acids, and amylase, which converts starch into glucose, as well as elastase, nattokinase, catalase and so on. Some of the names may be familiar to you.
These enzymes travel through the digestive tract and act effectively as digestive enzymes to digest the things we eat.

The natto bacillus itself has also been found to regulate intestinal functions.
There are more than a billion natto bacteria in each gram of natto. As one individual serving package of natto contains around 45g, this works out to an intake of 45 billion natto bacteria into the body at each meal.

Probiotics is the word that is used to describe living microorganisms that improve the balance in the intestinal environment of a host and therefore have a beneficial effect on the host, as well as the foods that contain these microorganisms. It is possible that the natto bacillus and the food that contains it, natto, also constitute an excellent probiotic.

Various microorganisms establish themselves in our intestines and form complex groups. The modality of these groups is called the intestinal flora, and among these microorganisms the bacteria are referred to as intestinal bacteria.
Several hundred varieties of intestinal bacteria are known to inhabit the human intestine. The natto bacillus acts to maintain the balance of intestinal bacteria and inhibit the putrefactive bacteria that are said to be harmful bacteria.
The natto bacillus also has the potential to inhibit disease-causing bacteria such as salmonella and Pseudomonas aeruginosa.

Another example of something that improves gut health that comes to mind is the lactic acid bacillus. In keeping with its image, the lactic acid bacillus is useful in maintaining the intestinal environment. Research has shown that the natto bacillus can not only coexist with the lactic acid bacillus in the intestine, it also aids the activity of the lactic acid bacillus.

The activity of the lactic acid bacillus is impeded in environments with active oxygen such as hydrogen peroxide, and its ability to propagate is impaired. However, the lactic acid bacillus lacks the enzymes and catalase needed to break down hydrogen peroxide.
What about the natto bacillus? It turns out that, yes, the natto bacillus is able to secrete catalase.
In experiments, it was observed that adding natto bacillus culture extract and catalase to lactic acid bacillus whose activity had become impaired and that was unable to propagate instantly revitalized the lactic acid bacillus and enabled it to propagate. Even when a different enzyme, nattokinase, was added, the propagative ability of the lactic acid bacillus was restored in the same manner.
Although these were only experiments, the results suggest that it is possible that the same thing may occur in the intestine.
_pdf (jst.go.jp)

The natto bacillus is a rod-shaped bacillus that resembles a baton with rounded ends. The size of each bacterium is 2-3 µm (1µm = 1/1000 of a mm). The baton-shaped bacillus stretches as far as it can and then splits as if being ripped apart, after which the process is repeated.
One bacterium becomes two, two become four, and so on. Each propagation takes only 30 minutes and doubles the quantity. Over the course of a single night, the number is increased by a factor of one million.

It should be noted that this is what happens in an environment that is favorable to natto.
This is the proliferation potential when nutrients derived from the boiled soybeans, moisture and a suitable temperature are all present.
However, if the environment is inhospitable to the bacillus...
... then the special ability of Bacillus subtilis, of which the natto bacillus is a member, is triggered. Each bacterium creates a tiny spore known as an endospore that is enclosed in a hard shell, and this endospore halts growth, sending the bacterium into hibernation until the conditions are more favorable. The hard shell is ultimately dissolved, but in its spore state, the bacillus does not die no matter how harsh the environment is. Even if there is no oxygen, or if it is heated for 30 minutes at a temperature of 100°C, or if it is placed in an alkaline or acidic solution, the spore does not die. This is why the natto bacillus is said to be tough.