Natto: Japan’s Stickiest Superfood and the Science Behind It
Natto being served over a small, pile of rice.
Natto is a traditional Japanese food made by fermenting cooked soybeans with Bacillus subtilis var. natto. Sticky, stringy, and famously pungent, it’s a love-it-or-hate-it food — but also one of the world’s most scientifically intriguing ferments. Beneath its threads lies a miniature lab of enzymes, vitamins, and live bacteria that have attracted decades of nutrition research.
Why Natto Matters
Fermentation changes soybeans dramatically. It concentrates several compounds with plausible effects on human health:
Menaquinone-7 (MK-7) — a long-chain form of vitamin K₂ important for bone and vascular health
Nattokinase (NK) — a fibrinolytic enzyme that can dissolve blood-clot proteins in lab tests
Poly-γ-glutamic acid (γ-PGA) — the sticky polymer responsible for natto’s texture
Small peptides, polyamines, and isoflavone aglycones — plant compounds made more absorbable through fermentation
Live B. subtilis strains — transient gut visitors that may support digestion
Together, these make natto a compact example of how traditional fermentation can turn simple beans into something functionally different.
Fermentation Microbiology: The Bacterium Behind It All
At the heart of natto is one microbe: Bacillus subtilis var. natto. When cooked soybeans are inoculated and kept warm for roughly a day, the bacteria grow, digest proteins, and produce the sticky γ-PGA that gives natto its tell-tale threads. They also generate MK-7 and the enzyme nattokinase — compounds that have become the focus of modern biomedical research.
Making natto sounds simple but hinges on fine control. Beans must be soaked, cooked until soft, and held at an even warm temperature so the bacteria can work. Small shifts in soak time, temperature, or starter strength change the outcome in texture and flavor.
Not all B. subtilis natto strains are the same. Some make more nattokinase or MK-7 than others, which explains why one brand can taste or feel different from another — and why supplements vary so widely. Fresh natto that hasn’t been pasteurized still contains live bacteria and active enzymes, while processed versions often lose both, leaving mainly the stable MK-7.
When produced with clean equipment and verified starter cultures, natto is considered safe. The bigger challenge for researchers is standardization: different strains and fermentation conditions make it difficult to compare studies or recommend reliable doses without consistent measurements of MK-7 and enzyme activity.
Bottom line: one bacterium transforms soybeans into a food rich in biologically active molecules — but strain choice and process details determine what ends up in the bowl.
Nutritional and Chemical Composition
A serving of natto offers the basic nutrition of soy — plant protein, fiber, and modest fat — plus a suite of compounds created only through fermentation.
Nattokinase is an enzyme that breaks down fibrin, the protein that helps form blood clots. Whether it survives digestion in meaningful amounts is still debated, but it remains one of natto’s signature molecules.
Menaquinone-7 (MK-7) is a long-chain form of vitamin K₂ produced during fermentation. It’s highly bioavailable and stays in the blood longer than vitamin K₁, helping activate proteins that build bone and keep calcium from depositing in arteries.
Poly-γ-glutamic acid (γ-PGA), the source of natto’s stringiness, also influences how nutrients bind water and minerals, potentially altering absorption.
Isoflavone aglycones and small peptides arise as the bacteria break soy proteins apart. These contribute to flavor and may have mild biological effects, such as antioxidant activity or gentle support of blood-pressure regulation.
Two practical notes:
Variation is real. Different soybeans, bacterial strains, and processing methods change how much MK-7 or nattokinase ends up in the final food.
Fresh vs. processed. Fresh, unpasteurized natto contains live bacteria and active enzymes; pasteurized or extracted versions lose those but retain MK-7.
In short: natto provides soy’s nutrients plus fermentation-made compounds — a useful vitamin K₂ source, an active enzyme, and more absorbable plant molecules — but amounts vary by product.
Natto being activated.
How It Works in the Body
Nattokinase: This bacterial enzyme breaks down fibrin in laboratory settings, suggesting potential support for healthy blood flow. What remains uncertain is how much survives digestion to act in the bloodstream.
MK-7 (Vitamin K₂): MK-7 activates proteins that direct calcium into bones and away from arteries. It’s well-absorbed, long-lasting in the body, and reliably increased by eating natto.
The Bacteria Themselves: B. subtilis spores can pass through the gut alive, producing enzymes and small compounds on the way. They don’t colonize permanently, so probiotic effects are likely mild and short-term.
Peptides and Isoflavones: Fermentation makes soy’s plant chemicals more absorbable. Some peptides show modest effects on blood-pressure-related enzymes, but these are subtle nutritional influences, not therapeutic ones.
γ-PGA: Mostly responsible for texture, though it may affect how water and nutrients move through the digestive tract — research is ongoing.
What’s certain: MK-7 is absorbed and active.
What’s probable: Nattokinase and the bacteria may offer small, supportive effects.
What’s unknown: Exactly how much of those actions translate into measurable long-term health outcomes.
What the Research Shows
Historical and Population Clues
Natto has been eaten in Japan for over a thousand years, particularly in eastern regions such as Ibaraki. Studies comparing Japanese regions find that people who eat more natto have higher vitamin K₂ intake, stronger activation of vitamin-K-dependent proteins, and fewer arterial calcifications. These are correlations but they hint that long-term natto consumption may contribute to bone and cardiovascular health.
Blood Clotting and Fibrinolysis
Small clinical studies show that nattokinase or natto extracts can increase blood-clot-dissolving activity in the blood. Results align with lab findings but vary by preparation and dose. Larger trials are still needed to see whether this translates into fewer clot-related events.
Blood Pressure and Circulation
Some studies report modest blood-pressure reductions after nattokinase supplementation or regular natto intake. Effects are generally small to moderate and depend on who’s studied and what form is used. For healthy adults, natto may gently support normal circulation but shouldn’t replace prescribed therapy.
Lipids and Metabolic Markers
Research on cholesterol and triglycerides is mixed: a few small trials show improvement, others show none. Differences in product quality and duration likely explain the inconsistency.
Bone Health and Vitamin K Pathways
MK-7 consistently raises blood markers showing that vitamin-K-dependent proteins are activated. Observational data link natto intake with fewer arterial calcifications and potentially stronger bones, but long-term fracture-reduction studies are limited.
Overall Assessment
Evidence is strongest for MK-7’s biological activity and its role in bone and vessel health. Findings on nattokinase, blood pressure, and lipids are promising but preliminary. Research is expanding, yet standardized trials using clearly defined natto preparations are still scarce.
Safety, Interactions, and Tolerance
For most healthy people, natto is safe. The main cautions are practical:
Blood-thinning medications: MK-7 can counteract warfarin, and nattokinase’s fibrinolytic action suggests caution with any anticoagulant or antiplatelet therapy.
Allergies: Made from soy; those with soy allergy should avoid it.
Digestive tolerance: Natto’s aroma and texture can be challenging at first. Mild digestive upset can occur in people unused to fermented foods.
Short-term studies show few adverse effects. As with any supplement-like food, moderation and context matter more than dosage.
Read More: Onigiri
How to Eat and Store It
Fresh natto has the most active enzymes and live bacteria. Pasteurized or concentrated products keep longer but lose those qualities — though they still supply vitamin K₂.
Traditional use: Natto is often mixed with soy sauce, mustard, or chopped green onions and eaten over rice. Stirring thoroughly improves texture and flavor. It can also be added to soups, salads, or omelets, though heat may reduce enzyme activity.
Serving size: In Japan, one small pack (40–50 g) per day is typical. Eating natto a few times per week is enough to raise MK-7 levels and support vitamin-K-dependent processes such as bone health.
Storage: Keep refrigerated and eat within a few days for best flavor and enzyme activity. Freezing extends shelf life but can alter texture. Processed natto or supplements last longer but contain fewer living elements.
Supplements: When Food Isn’t an Option
For those who can’t get used to the flavor or want consistent dosing, nattokinase or MK-7 supplements provide measured amounts of the active compounds. These can raise vitamin K₂ levels or offer standardized enzyme activity — but quality varies, and the same cautions about blood-thinning medications apply.
The Limits of Evidence
Even though natto has a strong traditional record and growing scientific interest, the evidence base still has gaps:
Most studies are small or short, measuring biochemical markers rather than hard outcomes like heart attacks or fractures.
Fresh natto, pasteurized products, and supplements differ significantly, so results from one can’t be applied directly to another.
Regional and historical observations can’t fully separate diet from genetics or lifestyle.
Still, the pattern is consistent: regular natto consumption reliably boosts vitamin K₂ intake and may gently support cardiovascular and bone health over time.
Read more: Ferments on Recipes & Roots
Practical Takeaway
Natto is a remarkable intersection of tradition and biochemistry. Its fermentation creates an enzyme that may help blood flow, a vitamin vital for bone and vessel health, and a texture unlike any other food. Eating it a few times a week is safe for most people and provides reliable vitamin K₂.
If you’re new to natto:
Start small and mix it well.
Pair it with familiar flavors like rice, soy sauce, or eggs.
Choose fresh natto for enzyme activity, or pasteurized for milder flavor and longer shelf life.
Consult a healthcare provider if you take blood thinners or have a soy allergy.
Nothing is a magic bullet, including natto, but it’s a fascinating example of how microbes can transform a humble ingredient into something nutritionally and culturally rich.
Natto is definitely a source of easy to digest protein that brings with it all the benefits of soybeans, or beans in general. It is nutrient dense and if consumed regularly will likely play a role in improved heart health.
Further Reading
Academic and Scientific Research
Afzaal, M., et al. (2022). “Nutritional Health Perspective of Natto: A Critical Review.” Foods. PubMed Central
Chen, H., et al. (2018). “Nattokinase: A Promising Alternative in Prevention and Treatment of Cardiovascular Diseases.” Frontiers in Pharmacology. PubMed Central
Elbanna, K., et al. (2024). “Poly(γ)-Glutamic Acid: A Unique Microbial Biopolymer with Diverse Applications.” Frontiers in Microbiology. PubMed Central
Xiang, A., et al. (2022). “Determination of 14 Isoflavone Isomers in Natto by UPLC-MS/MS.” Foods. PubMed Central
Kubo, Y., et al. (2021). “A High-Accuracy Method for Quantifying Poly-γ-Glutamic Acid Content in Natto.” Food Science and Technology Research. J-STAGE
Fang, M., et al. (2023). “Nattokinase: Insights into Biological Activity, Therapeutic Potential and Clinical Studies.” Fermentation. MDPI
Leñini, C., et al. (2023). “Probiotic Properties of Bacillus subtilis DG101 Isolated from the Traditional Japanese Fermented Food Natto.” Frontiers in Microbiology. PubMed Central
Books and Broader Context
Ashida, H., & T. Yamaguchi. Natto: The Japanese Superfood for Longevity and Health. Tokyo: Kodansha, 2019.
Hosoi, T. Fermented Foods of Japan: Science, Tradition, and Culture. Tokyo: Springer, 2020.
Shurtleff, W., & A. Aoyagi. History of Natto and Its Role in Japanese Culture and Health. Lafayette, CA: Soyinfo Center, 2012.
