Natto, Bacillus subtilis and Gut Health

Natto is not fermented by the lactic acid bacteria that make yogurt, kefir and sauerkraut. It is made by Bacillus subtilis var. natto, a bacterium that can wrap itself in a tough spore — a little survival capsule that rides through stomach acid and wakes up in the small intestine. A fresh pack carries hundreds of billions of these live cells. This page explains what that means for your gut, what human studies actually show (less than the marketing, more than nothing), and the small group of people for whom those same live bacteria are a real risk.

Table of Contents

  1. A Spore-Former, Counted by the Billion
  2. Surviving Stomach Acid: A Spore’s Journey
  3. What Human Studies Show
  4. Poly-γ-Glutamate and Other Natto Compounds
  5. Vitamin K2: Made by the Microbe
  6. Natto vs Sauerkraut, Yogurt and Kefir
  7. How Much Natto, and Pairing It With Other Ferments
  8. Who Should Be Careful
  9. Key Research Papers
  10. Connections
  11. Featured Videos

A Spore-Former, Counted by the Billion

Bacillus subtilis is a rod-shaped bacterium that has lived alongside people for as long as there has been soil, hay and rice straw. The natto variety, B. subtilis var. natto, is the strain line that Japanese cooks selected over centuries because it turns steamed soybeans into the sticky, stringy, savoury food we call natto. For the history of how that happened, see the Natto History page; for the full food-microbiology view, see Natto and Other Foods Made with Bacillus subtilis.

What makes this microbe unusual among food bacteria is the endospore. When conditions turn hostile — heat, dryness, acid, no food — the cell builds a thick, layered coat around a dehydrated copy of itself and goes dormant. Think of it as a seed rather than a plant: it does nothing, needs nothing, and can wait a very long time. When it lands somewhere warm, wet and nutritious, it germinates back into an active, dividing cell. Yogurt and sauerkraut bacteria cannot do this. They are always “awake”, and their survival through the stomach depends on sheer numbers and the protection of the food around them.

How many live bacteria are in a pack?

This number is often quoted loosely, so it is worth going to a measurement. A 2021 natto-quality study from a Japanese food-technology institute made natto the industrial way (spore solution sprayed on steamed soybeans, fermented at 39 °C, packed in 50 g cups) and counted living B. subtilis on agar plates. Freshly made natto held 7.5 × 109 colony-forming units (CFU) per gram — 7.5 billion live cells in every gram. After 20 days of refrigerated or cool storage the count fell about ten-fold, to 7.4–9.0 × 108 CFU per gram, and was still alive at every temperature tested (evidence tier: laboratory food measurement).

Multiply that out for a normal serving. A 40–50 g pack of fresh natto delivers roughly 300–375 billion live cells; an older pack near the end of its shelf life still delivers about 30–45 billion. For comparison, the B. subtilis probiotic capsules tested in the trials below gave 2 billion spores (in older adults) or 5 billion CFU (in a bloating trial) per day. One pack of natto, in other words, contains somewhere between several times and more than a hundred times the dose of a typical spore probiotic capsule. That is the single most important fact about natto as a “probiotic food”: the dose is enormous.

A plate count cannot tell you how many of those cells are spores and how many are active cells; both grow into colonies. In practice the coat of natto is a mix, and the spores are the part built to survive the trip through you.

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Surviving Stomach Acid: A Spore’s Journey

For most of the twentieth century B. subtilis was described as a soil organism that simply passed through animals. That picture changed when researchers started looking for it inside the gut itself. The most direct human evidence comes from a clever 2021 study in 11 people with an ileostomy — a surgical opening that lets the end of the small intestine drain into a bag, so scientists can sample what leaves the small bowel without a tube down the throat.

Participants swallowed spores of a probiotic B. subtilis strain. Within 3 hours, both spores and freshly germinated active cells were showing up in the ileum fluid. By six to eight hours, spores were present at about 97 million CFU per gram (dry weight) and active cells reached about 73 million CFU per gram at seven hours. In plain terms: the spores survived the stomach, survived bile, and germinated in the small intestine of living people (evidence tier: small randomised crossover human study). That study used a capsule strain, not natto, but the spore biology is the same species and the same mechanism.

The journey of a natto spore: a fresh pack holds about 300 to 375 billion live cells, spores survive stomach acid, germinate in the small intestine within 3 hours, and reach the colon with mixed human evidence, while a branch shows the rare bloodstream infection that can happen when the gut wall is breached. THE JOURNEY OF A NATTO SPORE each stop is tagged with the kind of evidence behind it THE PACK 7.5 billion CFU per gram when freshly made about 300–375 billion in a 40–50 g pack MEASURED · food lab STOMACH the spore coat resists acid and bile dormant spores pass through intact HUMAN · 11 ileostomy pts SMALL GUT spores germinate within 3 hours of swallowing active cells appear in the ileum HUMAN · 11 ileostomy pts COLON secretory IgA rose RCT subset of 44 people bloating: no overall effect RCT of 100 people MIXED · mostly capsules IF THE GUT WALL IS BREACHED perforation, cancer chemotherapy, frail old age in hospital → the same live cells can reach the blood (bacteremia) — rare 70 of 4,634 positive blood cultures were B. subtilis; 69 were natto strain CASE SERIES · CASE-CONTROL built to survive the spore is why it reaches the gut evidence thins later benefits are unproven

The figure shows why natto is different and also where the honest uncertainty sits. The first three steps are solid: the bacteria are there in huge numbers, the spores survive, and they germinate. Step four — what those germinated cells do for the colon, the microbiome and the immune system — is where the human evidence is thin and mixed, as the next section explains. The red branch is the price of carrying live bacteria into a body whose defences are down.

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What Human Studies Show

Here is the frustrating part. There are remarkably few randomised trials that feed people natto and measure their gut. Most human evidence comes from B. subtilis probiotic capsules, which contain the same species at a much lower dose. The results below are reported as the trials reported them, including the outcomes that did not move.

Older adults and the immune system (RCT, primary outcome not met)

A French trial randomised 100 healthy adults aged 60–74 to a placebo or 2 billion B. subtilis spores a day, taken in 10-day courses repeated four times over a 4-month winter. The main question was whether the spores cut the number of days with colds, chest infections or stomach bugs. They did not significantly: 5.1 days in the probiotic group versus 6.6 days on placebo, a gap that could easily be chance (P = 0.20). In the subset of 44 people who gave stool and saliva samples, however, the spore group showed significantly higher secretory IgA — the antibody that coats the gut and mouth lining like a first line of defence — and a post-hoc look suggested fewer respiratory infections. Evidence tier: RCT; immune-marker change in a subset, clinical benefit not proven.

Bloating, gas and bowel habits (RCT, primary outcome not met)

A North American trial randomised 100 healthy adults to a placebo or 5 billion CFU of a B. subtilis strain daily for 4 weeks, tracking bloating, abdominal discomfort, gas and bowel habits in daily diaries. Across everyone, there was no significant difference from placebo. Men in the spore group did report fewer days of bloating and gas, but subgroup findings like that are a hypothesis, not a result. The spores were well tolerated, with blood tests staying normal. Evidence tier: RCT; no overall benefit, subgroup signal only.

Natto eaters and butyrate-producing bacteria (cross-sectional)

In a Japanese cohort of 185 people studied for barley intake and gut health, the people who ate a lot of barley and stayed non-obese also ate notably more natto than the others, and their stool carried more Butyricicoccus and Subdoligranulum — bacteria that make butyrate, the short-chain fatty acid that feeds the cells lining the colon. The authors suggest that B. subtilis from natto may help break down fibre so butyrate producers can thrive. That is a reasonable idea, but this was a single snapshot of free-living people: it shows that natto eating travels with a certain gut profile, not that natto caused it. Evidence tier: cross-sectional association.

Fermented foods as a group (RCT)

The strongest whole-food evidence is for fermented foods in general, not natto alone. In a 17-week Stanford trial (18 people per arm), healthy adults who steadily raised their intake of fermented foods saw their gut microbiome diversity rise and many inflammatory markers fall; a high-fibre comparison diet did not produce the same diversity shift over that time. Natto was not the test food, but the trial supports the general principle that eating a variety of live fermented foods changes the gut ecosystem in a measurable, favourable direction. Evidence tier: small RCT.

The fair summary

Animal and test-tube studies make bolder claims, but those findings are a reason to run human trials, not a substitute for them.

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Poly-γ-Glutamate and Other Natto Compounds

The live bacteria are only half the story. While they ferment the beans, they also manufacture new substances that stay in the food whether or not the cells survive.

Poly-γ-glutamate: the strings

Those long, sticky threads when you stir natto are mostly poly-γ-glutamate (PGA) — a long chain of glutamic acid units made by the bacterium. PGA grabs calcium and keeps it dissolved, which led researchers to ask whether it helps people absorb calcium.

In a small but well-measured British crossover study, 24 post-menopausal women drank orange juice containing 200 mg of tracer-labelled calcium, once with and once without 60 mg of PGA. Calcium absorption was 39.1% with PGA versus 34.6% without — a modest but statistically significant gain, and largest in the women who absorbed calcium poorly to begin with. Evidence tier: single-dose human crossover trial. It used purified PGA, not natto, and it measured one meal, not bone. It does make a plausible case that the sticky part of natto is doing something useful alongside the vitamin K2 that natto is famous for (see Natto for Bone Density).

Could PGA act like a prebiotic — food for helpful gut bacteria? Animal studies have explored the idea, but we found no human trial testing it directly. Evidence tier: animal only. Treat “natto is a prebiotic” as an open question.

Nattokinase and other products

The bacterium also secretes nattokinase, an enzyme that breaks down fibrin, the protein mesh of blood clots. That is a cardiovascular topic rather than a gut one, and it carries a bleeding caution with blood thinners; see Nattokinase and Fibrinolysis and the Nattokinase page. Fermentation also breaks soy proteins into smaller peptides and free amino acids — part of why natto tastes savoury and is easier to digest than plain boiled soybeans — and produces the ammonia note in its smell.

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Vitamin K2: Made by the Microbe

Natto’s best-documented nutritional gift is a direct product of B. subtilis metabolism: menaquinone-7 (MK-7), the long-lasting form of vitamin K2. Soybeans themselves contain almost none; the bacterium makes it during fermentation. Vitamin K2 activates proteins that put calcium into bone and keep it out of artery walls (full detail on Natto for Vitamin K2 (MK-7) and Vitamin K2).

How strong is the effect on the body? A study of post-menopausal women found average blood MK-7 of 5.26 ng/mL in Tokyo, where natto is eaten often, 1.22 ng/mL in Hiroshima, where it is eaten rarely, and 0.37 ng/mL in British women — roughly a fourteen-fold gap between Tokyo and Britain. Eating natto produced a marked, sustained rise in blood MK-7, and across Japanese prefectures more natto eating went with fewer hip fractures in women (evidence tier: cross-sectional and ecological, with a feeding test). A Dutch food-analysis study likewise found that after eating natto, circulating vitamin K2 rose to levels about 10 times higher than the vitamin K1 reached after a meal of spinach (evidence tier: small human feeding study).

This is also where natto differs most sharply from lactic-acid ferments. In that same food database, vitamin K2 was found mainly in meat, liver, butter, egg yolk, cheese, curd cheese and natto. Yogurt, kefir and sauerkraut are not significant K2 sources by comparison — natto stands in a class of its own. The flip side matters: the same vitamin K that helps bone is why people on warfarin must not eat natto casually (see Who Should Be Careful).

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Natto vs Sauerkraut, Yogurt and Kefir

“Fermented food” is a category, not a single thing. Natto and the lactic-acid ferments are made by different microbes doing different chemistry, so they bring different things to the table. The matrix below sets them side by side.

A comparison matrix of natto, sauerkraut, yogurt and kefir across main microbe, whether the microbe forms spores, vitamin K2 content and human trial evidence, showing natto alone is a spore-former and a rich vitamin K2 source while the human trial evidence is thin for every food except yogurt. FOUR FERMENTS, FOUR DIFFERENT MICROBES natto is the odd one out on two of four rows NATTO SAUERKRAUT YOGURT KEFIR MAIN MICROBE Bacillus subtilis var. natto lactic acid bacteria L. plantarum, L. brevis lactic acid bacteria S. thermophilus and kin lactic acid bacteria plus yeasts SPORE-FORMER? yes rides through acid no no no survival relies on numbers and the food around them VITAMIN K2 very high, MK-7 Tokyo 5.26 ng/mL serum minor minor minor not among the main K2 foods in analyses HUMAN TRIALS capsule RCTs of the species; few on natto a pilot RCT, 34 IBS patients the most studied of the four 16 RCTs reviewed, 12 at high risk of bias different microbes, different jobs natto adds a spore-former and vitamin K2 that lactic ferments do not; eat them together rather than choosing one

What each row means

The practical message is the one in the figure: these foods are complementary, not interchangeable. See our pages on Sauerkraut, Kefir and Kimchi.

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How Much Natto, and Pairing It With Other Ferments

Natto is sold in small single-serving cups, usually 40–50 g each, and that is the amount most Japanese eaters have at a meal — typically at breakfast, over rice. One pack is a sensible daily serving. There is no evidence that eating several packs a day gives more gut benefit, and remember the arithmetic from the first section: a single fresh pack already delivers hundreds of billions of live cells.

Keeping the bacteria alive

Building a fermented-food plate

Because natto and lactic ferments bring different microbes, the best approach is variety. Fermented foods are a priority on this site, and natto fits naturally into a whole-food, fermented-food routine:

If the taste and texture are a hurdle, the Acquired-Taste Tips page has a step-by-step approach, and How to Make Natto covers making it at home. For the full nutrient breakdown see Natto Nutrients.

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Who Should Be Careful

For healthy people, natto has been eaten daily by millions for centuries. But “live bacteria by the hundred billion” cuts both ways, and recent Japanese research has shown that B. subtilis var. natto is not always harmless.

Bloodstream infection in people with weakened defences

Who should avoid natto, or ask their care team first: people receiving cancer chemotherapy or with very low white-cell counts; transplant recipients and others on strong immune-suppressing drugs; people with a known bowel perforation, recent bowel surgery or active bowel cancer; and frail older adults in hospital. Spore-based B. subtilis probiotic capsules deserve the same caution, for the same reason.

The other documented cautions

The full safety picture is on Natto Safety and Interactions.

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Key Research Papers

  1. Kubo Y, Noguchi T, Kimura K (2021). Storage temperature and quality changes of natto. Food Science and Technology Research. — doi:10.3136/fstr.27.497
  2. Colom J, Freitas D, Simon A, Brodkorb A, Buckley M, Deaton J, et al. (2021). Presence and Germination of the Probiotic Bacillus subtilis DE111® in the Human Small Intestinal Tract: A Randomized, Crossover, Double-Blind, and Placebo-Controlled Study. Frontiers in Microbiology. — PubMed PMID: 34408741
  3. Lefevre M, Racedo SM, Ripert G, Housez B, Cazaubiel M, Maudet C, et al. (2015). Probiotic strain Bacillus subtilis CU1 stimulates immune system of elderly during common infectious disease period: a randomized, double-blind placebo-controlled study. Immunity & Ageing. — PubMed PMID: 26640504
  4. Penet C, Kramer R, Little R, Spears JL, Parker J, Iyer JK, et al. (2021). A Randomized, Double-blind, Placebo-controlled, Parallel Study Evaluating the Efficacy of Bacillus subtilis MB40 to Reduce Abdominal Discomfort, Gas, and Bloating. Alternative Therapies in Health and Medicine. — PubMed PMID: 31719214
  5. Maruyama S, Matsuoka T, Hosomi K, Park J, Murakami H, Miyachi M, et al. (2024). High barley intake in non-obese individuals is associated with high natto consumption and abundance of butyrate-producing bacteria in the gut: a cross-sectional study. Frontiers in Nutrition. — PubMed PMID: 39545049
  6. Wastyk HC, Fragiadakis GK, Perelman D, Dahan D, Merrill BD, Yu FB, et al. (2021). Gut-microbiota-targeted diets modulate human immune status. Cell. — PubMed PMID: 34256014
  7. Tanimoto H, Fox T, Eagles J, Satoh H, Nozawa H, Okiyama A, et al. (2007). Acute effect of poly-gamma-glutamic acid on calcium absorption in post-menopausal women. Journal of the American College of Nutrition. — PubMed PMID: 18187428
  8. Kaneki M, Hodges SJ, Hosoi T, Fujiwara S, Lyons A, Crean SJ, et al. (2001). Japanese fermented soybean food as the major determinant of the large geographic difference in circulating levels of vitamin K2: possible implications for hip-fracture risk. Nutrition. — PubMed PMID: 11369171
  9. Schurgers LJ, Vermeer C (2000). Determination of phylloquinone and menaquinones in food. Effect of food matrix on circulating vitamin K concentrations. Haemostasis. — PubMed PMID: 11356998
  10. Nielsen ES, Garnås E, Jensen KJ, Hansen LH, Olsen PS, Ritz C, et al. (2018). Lacto-fermented sauerkraut improves symptoms in IBS patients independent of product pasteurisation – a pilot study. Food & Function. — PubMed PMID: 30256365
  11. Kairey L, Leech B, El-Assaad F, Bugarcic A, Dawson D, Lauche R (2023). The effects of kefir consumption on human health: a systematic review of randomized controlled trials. Nutrition Reviews. — PubMed PMID: 35913411
  12. Sada RM, Yamamoto G, Hamaguchi S, Kuroda E, Okura A, Cai M, et al. (2025). The Majority of Bacillus subtilis Strains Isolated From Blood Cultures Were Derived From Traditional Japanese Fermented Soybeans Natto: A Single-center Retrospective Study. Open Forum Infectious Diseases. — PubMed PMID: 41018695
  13. Aoyagi R, Okita K, Uda K, Ikegawa K, Yuza Y, Horikoshi Y (2023). Natto intake is a risk factor of Bacillus subtilis bacteremia among children undergoing chemotherapy for childhood cancer: A case-control study. Journal of Infection and Chemotherapy. — PubMed PMID: 36585273
  14. Hashimoto T, Yahiro T, Khan S, Kimitsuki K, Hiramatsu K, Nishizono A (2023). Bacillus subtilis Bacteremia from Gastrointestinal Perforation after Natto Ingestion, Japan. Emerging Infectious Diseases. — PubMed PMID: 37735785

PubMed Topic Searches

  1. PubMed: Bacillus subtilis natto and gut microbiota
  2. PubMed: Poly-γ-glutamic acid in natto
  3. PubMed: Bacillus subtilis bacteremia and natto

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Connections

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