A samurai's spoiled horse feed became natto, and a staph fighter lives inside it
Picture northern Japan, around the year 1086. Samurai under the warlord Minamoto no Yoshiie are boiling soybeans for their horses. Then the enemy attacks.
So the men scoop the hot beans into straw sacks and run. Days pass before anyone opens them. By then the beans are sticky, stringy, and smell like old socks. A hungry soldier tastes them anyway… and likes them.
That, the legend goes, is how Japan got natto. Nine centuries later, scientists found that the germ in those sacks can push staph out of your gut. Staph is the bug behind boils and wound infections, including drug-resistant MRSA. And one number from Thailand shows how well it works.
That zero came from stool samples, not a lab dish. So who collected them, and where?
An NIH staph lab tested stool from rural Thailand, then moved the experiment into mice
The lab belongs to Michael Otto at the NIH. In 2018, his group worked with doctors in Thailand to collect stool from 200 healthy people in farm villages.
About half of them, 101 people, had Bacillus, the natto germ, in their gut. Staph showed up in 25 others. Not one person had both.
Next, the team turned to mice. Normal Bacillus spores wiped staph out of their guts. A lab-made strain missing one compound did nothing. So what is that missing piece, and how does it beat staph without killing it?
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Staph takes a head count before it settles in, and a Bacillus compound called fengycin scrambles the signal
Every staph bug leaks a tiny chemical signal into the gut. As it builds up, the bugs can tell the crowd is big enough to switch on the genes they need to grow and hang on.
Scientists call this quorum sensing. Fengycin gets in the way by blocking the staph signal. So every staph bug acts like it's alone… and none of them dig in.
Nothing gets poisoned. Staph just can't get organized, so it washes out with everything else you flush. And the exact Bacillus behind fengycin sits in foam tubs in the freezer aisle.
Bacillus subtilis: the microbe inside every tub of natto
It lives on hay, rice straw and soil. So the warm beans in those samurai sacks turned into natto.
B. subtilis packs itself into tough little spores. These ride out the stomach acid that kills most germs. Then they wake up and grow in your gut before passing through.
About 1 in 3 people carry staph in their nose, says the CDC. Many staph infections start there. In 2023, Otto's team gave 115 Thai adults a daily Bacillus capsule or a dummy pill for four weeks. Gut staph dropped 96.8% in the capsule group, and nose staph fell 65.4%.
That capsule is not on store shelves yet. But natto isn't the only food this bacterium makes.
Four fermented bean foods from Asia and West Africa, starting with natto
Home cooks have fermented beans this way for centuries. Nobody has tested these foods against staph yet. Still, each one is made by B. subtilis or its close cousins.
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Natto (Japan) Whole soybeans that pull into long threads. Look for Mizkan in the freezer aisle. |
Cheonggukjang (Korea) Fast-fermented soybeans cooked into a thick, funky stew. |
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Thua nao (Thailand) Thai soybean cakes, often pounded into chili paste. |
Dawadawa (West Africa) Fermented locust beans used to season soups and sauces. |
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Natto is the easiest of the four to find in the US. And there is a trick to eating it the first time.
Buy frozen natto and stir one tub 30 times before you eat it
Asian grocers like H Mart stock frozen natto in small tubs, usually three to a pack. Thaw one in the fridge overnight. Open it, add the little sauce and mustard packets, and stir hard until it foams. Spoon it over warm rice. Start with half a tub if the smell throws you.
| ❎ Toss the tub because the strings look weird | ✅ Stir the strings in with the sauce and eat them |
That stringy goo is spun by the Bacillus itself. Each thread is a sign the fermenting worked.
A samurai ran from a fight and saved his beans.
Now the microbe inside them may help your gut win a battle of its own.
Natto strings are a chain called poly-gamma-glutamic acid, made by B. subtilis. It holds so much water that skin care brands now sell it in serums labeled "polyglutamic acid," right next to hyaluronic acid.
