Foods that Contain Bacillus subtilis Explained

November 15, 2025 •

4 min read

According to a review published by the National Institutes of Health, the consumption of fermented soybean products has a long history in East and South Asian countries, where Bacillus subtilis is frequently used. This beneficial probiotic bacterium, and the potent spores it forms, are found primarily in traditional fermented soybean products but can also be present in other foods and supplements.

Quick Summary

This article details specific foods naturally containing Bacillus subtilis, focusing on traditional fermented soybean products like nattō and certain Southeast Asian fermented foods. It also discusses how this probiotic supports gut health and enhances nutritional value.

Key Points

Natto (Japanese Fermented Soybeans): Nattō is the most well-known food source of Bacillus subtilis, specifically the var. natto strain, responsible for its distinct flavor and health-promoting compounds.
Regional Fermented Legumes: Traditional fermented legume dishes from other parts of Asia and Africa, such as Nepalese kinema, Thai thua nao, and West African ugba, also contain Bacillus species.
Select Probiotic Drinks and Dairy: Certain commercial probiotic drinks and some traditional dairy products, like traditional buttermilk, can be sources of Bacillus subtilis through intentional addition or natural presence.
Resilient Probiotic Action: Bacillus subtilis forms heat-resistant spores, enabling it to survive harsh processing and stomach acid to reach and colonize the gut effectively.
Multiple Health Benefits: Consuming foods with Bacillus subtilis supports a balanced gut microbiome, enhances immune function, and improves nutrient absorption by producing digestive enzymes.
Supplements are Also a Source: For those who dislike the taste of natto, supplements are a common alternative for consuming beneficial Bacillus subtilis strains.

Traditional Fermented Soybean Products

When it comes to identifying which foods contain Bacillus subtilis, the most prominent and reliable source is a group of traditional fermented soybean foods. These products, particularly well-known in Asian and African cultures, leverage the potent fermentation properties of Bacillus species to enhance flavor, nutritional content, and digestibility.

Natto (Japan)

Perhaps the most famous food containing Bacillus subtilis is natto, a traditional Japanese fermented soybean dish. The specific strain used, Bacillus subtilis var. natto, is responsible for its characteristic slimy texture and strong, pungent flavor. The fermentation process of natto is a unique example of how a single microbial species can transform a simple foodstuff into a nutrient-dense powerhouse. Natto is a staple of many Japanese breakfasts, often served with rice, and is celebrated for its high content of vitamins and beneficial enzymes like nattokinase.

Kinema (Nepal) and Thua Nao (Thailand)

In Nepal, a similar fermented soybean product called kinema is made using Bacillus subtilis. In Thailand, the equivalent product is thua nao. These foods demonstrate the widespread, traditional use of this bacterium across various Asian cuisines for centuries. The fermentation process breaks down complex compounds in the soybeans, making the nutrients more bioavailable and reducing anti-nutritional factors.

African Fermented Foods

The use of Bacillus species, including B. subtilis, is not limited to Asia. In West African countries like Nigeria, traditionally fermented foods rely on Bacillus strains. For instance, dawadawa and ugba are fermented legume products that benefit from the action of these bacteria, which enrich the food with unique flavors and improved nutritional profiles.

Fermented Condiments and Other Foods

While soy is the primary host, some other fermented products and probiotic foods may contain Bacillus subtilis, particularly certain commercial formulations.

Miso and Tempeh

Traditional miso paste, a savory Japanese seasoning, is created by fermenting soybeans with salt and koji fungus, and often contains Bacillus strains. Tempeh, an Indonesian fermented soybean cake, is primarily fermented with a different fungus but can also host Bacillus species depending on the preparation.

Dairy and Probiotic Drinks

Some commercial probiotic products and supplements intentionally add spore-forming Bacillus subtilis for its resilience to harsh processing and stomach acid. Certain probiotic drinks or milks fermented with specific Bacillus strains are being developed to produce functional products, such as milk with thrombolytic properties. Traditional buttermilk, especially from some regions of India and Pakistan, may also contain naturally occurring Bacillus species.

Potential Health Benefits from Foods Containing Bacillus subtilis

Eating foods that contain Bacillus subtilis can offer several health benefits, particularly related to digestive and immune health. The spore-forming nature of Bacillus subtilis allows it to survive the journey through the digestive system and colonize the gut, where it produces enzymes and helps balance the microbiome.

Support for Gut Health: B. subtilis contributes to a balanced gut microbiome by promoting the growth of beneficial bacteria like Lactobacillus and Bifidobacterium, while inhibiting the growth of pathogens. This can lead to reduced gastrointestinal issues such as constipation, diarrhea, and bloating.
Enhanced Immunity: By modulating the gut microbiome, B. subtilis can also stimulate immune responses, helping the body fight off illness. It has been shown to enhance immunity markers and reduce inflammation.
Improved Nutrient Absorption: The bacteria produce enzymes that help break down complex macromolecules, such as proteins and indigestible polysaccharides, into smaller, more easily absorbed components.

Comparison of Fermented Food Sources


Feature	Natto	Kinema / Thua Nao	Certain Probiotic Milks	Fermented Soybean Meals (e.g., Miso, Tempeh)
Primary Fermenting Agent	Bacillus subtilis var. natto	Bacillus subtilis species	Specific Bacillus subtilis strains (often added)	Diverse microbes, including Bacillus species
Origin	Japan	Nepal / Thailand	Varies (Traditional and modern)	Primarily Indonesia / Japan
Health Benefits	High in vitamin K2 and nattokinase for cardiovascular and bone health.	Improves nutrient availability and sensory profile.	Potential for specific functional effects, like antithrombotic activity.	Increases nutrient bioavailability and contains beneficial compounds.
Flavor Profile	Strong, pungent, acquired taste.	Flavor and aroma vary by regional preparation.	Varies, potentially mild and palatable.	Savory, umami flavor (miso); earthy and nutty (tempeh).

Conclusion

Foods containing Bacillus subtilis are predominantly traditional fermented products, with Japanese nattō being the most prominent example. This powerful probiotic is also found in other regional fermented soybean products like kinema and thua nao, and certain engineered probiotic dairy products. The spore-forming ability of B. subtilis ensures its survival and activity within the gut, where it supports digestive health, balances the microbiome, and boosts immune function. While these traditional foods offer a natural source, modern probiotic supplements also leverage the robustness of Bacillus subtilis for targeted health benefits. Understanding these dietary sources allows for informed choices aimed at supporting overall gut and systemic wellness. For those with compromised immune systems, medical advice should be sought before consuming live probiotic foods or supplements.

Frequently Asked Questions

Bacillus subtilis is a spore-forming probiotic, meaning it can create a protective shell to survive harsh conditions like high heat and stomach acid. Other common probiotics, such as Lactobacillus, do not form spores and are therefore more sensitive to these environmental stresses.

No, fermentation does not guarantee the presence of Bacillus subtilis. While many fermented foods are rich in probiotics, the microbial cultures used vary widely. For example, yogurt relies primarily on Lactobacillus and Bifidobacterium, while natto specifically utilizes Bacillus subtilis.

Yes. While nattō is a concentrated source, you can get Bacillus subtilis through specific probiotic supplements that feature spore-forming strains. It is also found in other traditional fermented foods, but identifying the specific presence can be difficult.

Most healthy individuals can safely consume Bacillus subtilis in fermented foods. However, severely immunocompromised individuals, like those undergoing chemotherapy, are advised to exercise caution with some raw fermented foods containing live bacteria due to a potential risk of infection.

Key health benefits include promoting a balanced gut microbiome by aiding beneficial bacteria, boosting the immune system's response, reducing inflammation, and producing enzymes that enhance the digestion and absorption of nutrients.

Bacillus subtilis var. natto is a specific variant used for fermenting soybeans into nattō. This strain is responsible for the unique properties of nattō, such as its vitamin K2 content and the enzyme nattokinase, which is known for its cardiovascular benefits.

While kimchi and kombucha are excellent sources of diverse probiotics, they are not primarily fermented by Bacillus subtilis. They typically contain lactic acid bacteria and yeasts, though some minor Bacillus species may be present depending on the preparation.