What Kind of Probiotic Is in Natto?

December 22, 2025 •

4 min read

As a fermented superfood, natto is packed with beneficial microorganisms that contribute to its impressive health benefits. The probiotic responsible for transforming soybeans into the signature slimy, pungent Japanese dish is a powerful, heat-resistant bacteria called Bacillus subtilis var. natto. Unlike many common probiotic strains, its spore-forming nature allows it to withstand the harsh journey through your digestive system, reaching the intestines alive and ready to work.

Quick Summary

The probiotic found in natto is Bacillus subtilis var. natto, a resilient spore-forming bacterium that effectively survives the digestive process. It populates the gut, promoting a balanced microbiota, inhibiting harmful pathogens, and supporting immune function.

Key Points

Bacillus subtilis natto is the Probiotic: The specific probiotic bacterium found in natto is Bacillus subtilis var. natto.
Spore-Forming and Resilient: This probiotic is spore-forming, meaning it can survive the high heat of fermentation and the harsh acidic conditions of the stomach to reach the intestines effectively.
Supports Gut Microbiota: Instead of just adding new bacteria, Bacillus subtilis natto nourishes and supports the native beneficial gut flora, like Lactobacillus and Bifidobacterium.
Produces Nattokinase: The fermentation process yields the enzyme nattokinase, which is known for its cardiovascular health benefits.
Enriches Vitamin K2: Natto is one of the richest food sources of Vitamin K2, produced by the probiotic, which is vital for bone and heart health.
Inhibits Pathogens: The bacteria and its byproducts have antimicrobial properties that can help suppress the growth of harmful bacteria in the gut.

The Dominant Probiotic: Bacillus subtilis var. natto

Natto's renowned health properties are primarily due to the potent probiotic bacteria used in its fermentation: Bacillus subtilis var. natto. This strain is a robust, spore-forming bacterium, which is key to its effectiveness as a probiotic. The spores are encased in a protective outer coat, allowing them to withstand harsh conditions like high heat during the soybean steaming process and the acidic environment of the stomach. This resilience ensures a high number of live, active bacteria reach the intestinal tract, ready to colonize and exert their health-promoting effects.

How Bacillus subtilis natto Boosts Gut Health

Upon arriving in the intestines, Bacillus subtilis var. natto plays a significant role in modulating the gut microbiota. Rather than simply adding to the bacterial population, it actively supports and nourishes the existing beneficial flora, such as Bifidobacterium and Lactobacillus, which are crucial for digestive and immune health. By influencing the balance of bacteria, it creates a healthier and more diverse microbial environment.

Enhanced Microbiota Diversity: Studies have shown that consuming natto can increase the relative abundance of beneficial gut bacteria, leading to a more diverse and resilient gut ecosystem.
Pathogen Inhibition: B. subtilis natto produces antimicrobial compounds that can inhibit the growth of harmful bacteria, helping to suppress pathogens like E. coli and Salmonella.
Enzyme Production: The fermentation process and the bacteria itself produce various enzymes, including proteases that aid in digestion. One of the most famous is nattokinase, which offers powerful cardiovascular benefits.
Improved Digestion: The presence of this probiotic can help alleviate digestive issues like bloating and constipation by regulating the bacterial balance in the gut.

Comparison: Natto Probiotics vs. Other Fermented Foods

Not all probiotics are created equal. The unique characteristics of Bacillus subtilis var. natto set it apart from the more common probiotics found in dairy products like yogurt or other fermented foods like kimchi.


Feature	Natto (Bacillus subtilis natto)	Yogurt (Lactobacillus, Bifidobacterium)	Kimchi (Lactobacillus)
Probiotic Type	Spore-forming bacteria	Non-spore-forming bacteria	Non-spore-forming bacteria
Survival in Digestion	Highly resistant to stomach acid due to spores, ensuring high viability in the gut.	Variable survival rate; can be sensitive to stomach acid and digestive enzymes.	Sensitive to stomach acid; fewer live bacteria may reach the intestines.
Key Enzymes Produced	Nattokinase (unique to natto), amylase, and proteases.	Lactase and other enzymes aiding lactose digestion.	Primarily lactic acid.
Bioactive Compounds	High Vitamin K2 (menaquinone-7), poly-gamma-glutamic acid (PGA), nattokinase.	Calcium, peptides, and other metabolites.	Vitamins A and C, and various phenolic compounds.
Interaction in Gut	Activates and supports native gut bacteria like Bifidobacterium and Lactobacillus.	Contributes new strains directly.	Supports gut health through lactic acid bacteria.

The Journey from Soy to Superfood

The creation of natto is a carefully controlled process that enables the specific probiotic bacteria to thrive. It starts with washing and soaking soybeans, which are then steamed under pressure to become soft. This steaming process also serves a crucial purpose: it sterilizes the beans, killing off any unwanted bacteria that could interfere with the fermentation. Once the beans have cooled to the ideal temperature, the Bacillus subtilis var. natto culture is sprayed onto the cooked beans. The inoculated beans are then incubated for 16–24 hours at a warm temperature (around 40°C), where the bacteria multiply and ferment the soybeans. This fermentation creates the product's distinctive sticky, web-like strands and potent flavor. Finally, the natto is cooled and left to mature, which further develops its signature flavor profile and stabilizes the beneficial compounds. It's this precise process that delivers a product teeming with active probiotic power.

The Overall Health Impact of Natto’s Probiotic

The health benefits of Bacillus subtilis natto go far beyond simple digestion. Regular consumption of this unique probiotic can have a wide-ranging, positive impact on overall wellness. The bacterium's ability to modulate the intestinal microflora is linked to enhanced immune system function, as a balanced gut is integral to a robust immune response. Research also suggests that the enzymes produced during fermentation, including nattokinase, play a significant role in cardiovascular health by helping to maintain healthy blood flow. Additionally, the probiotic facilitates the creation of vitamin K2 (menaquinone-7), a nutrient critical for bone health that is otherwise rare in plant-based foods.

Conclusion

In summary, the probiotic in natto is the highly resilient, spore-forming Bacillus subtilis var. natto. This unique strain survives the digestive tract to profoundly and positively impact gut health by modulating the microbiota, inhibiting harmful pathogens, and enhancing nutrient availability. Combined with the other bioactive compounds it produces, such as nattokinase and vitamin K2, this probiotic elevates natto from a simple fermented food to a genuine superfood with significant benefits for digestive, immune, and cardiovascular health. While the flavor may be an acquired taste, the powerful probiotic effect of Bacillus subtilis natto is a compelling reason to consider including this traditional Japanese food in your diet. For those seeking to boost their gut health with a uniquely potent probiotic, natto provides an exceptional option worth exploring.

Visit Revolution Fermentation for a guide to making your own natto at home.

Frequently Asked Questions

Yes, the probiotics are different. Natto contains the spore-forming Bacillus subtilis var. natto, which is uniquely resilient to heat and stomach acid. Yogurt typically contains non-spore-forming bacteria like Lactobacillus and Bifidobacterium, which have a lower survival rate through the digestive tract.

Nattokinase supplements contain the enzyme, but not necessarily the live bacteria. For the full probiotic benefits of the living Bacillus subtilis natto culture, it is best to consume the whole food. However, some supplements may include the live bacteria in spore form.

The spores of Bacillus subtilis natto pass through the stomach safely and germinate in the intestines. Here, the active bacteria colonize the gut and help balance the microbiota, produce beneficial enzymes, and support the immune system.

No, the probiotic content varies significantly among different fermented foods. While many fermented foods contain beneficial bacteria (e.g., Lactobacillus in kimchi or yogurt), only natto is fermented with the specific, spore-forming Bacillus subtilis var. natto.

While generally safe, natto may not be suitable for some individuals. People with a soy allergy or intolerance should avoid it. Additionally, those on blood-thinning medication should consult a doctor before consuming natto due to its high Vitamin K2 and nattokinase content, which can affect blood clotting.

For optimal probiotic benefits, consuming natto uncooked is recommended to ensure the bacteria remain active. Heat can damage or kill some of the active cultures. Stirring natto vigorously can also increase its potent properties.

Yes, children can eat natto, and it can be a nutritious food for them. However, as with any new food, it's best to introduce it in small amounts to check for tolerance. The same precautions apply regarding soy allergies and specific medical conditions.

Yes, fresh natto contains the highest concentration of live, active cultures. While the probiotic spores are resilient, the maturation and storage process affects the overall activity. Checking the expiration date and storing it properly in the refrigerator helps maintain its potency.