World’s Oldest Bio-Business Is Japan’s Seed Koji Retailing, Mold Used to Make Fermented Products like Sake, Miso, Soy Sauce

By Tatsuya Kimura / Yomiuri Shimbun Staff Writer

16:56 JST, March 9, 2026

Sake, miso and soy sauce are all fermented products made with Aspergillus oryzae, or koji mold. Although koji mold has been a key component in Japanese cuisine for a long time, there are now only 10 “tane koji” (seed koji) retailers nationwide that supply koji mold to domestic breweries and fermented food manufacturers.

Creating pure koji cultures and collecting koji spores require refined skills. In Japan, such skills have been passed down since the Muromachi period (1336-1573).

Curbing bacteria growth

Down a narrow street leading to Kiyomizudera temple in Kyoto there is an old store named Hishiroku that sells seed koji, also known as koji starters, that contain koji spores. Exactly when the seed koji shop was founded is unknown, but it is said to have a history of more than 300 years.

“I don’t have the audacity to think we are supporting Japanese cuisine, but I am committed to maintaining the quality of our products,” said Akihiko Sukeno, the company’s president.

Hishiroku sells seed koji to about 2,000 brewing and fermented food companies nationwide that make products such as sake, soy sauce, miso, vinegar and shochu liquor.

Seed koji is grown by sprinkling koji mold onto steamed rice and culturing the rice for five days in an environment with a temperature of 30 C and humidity of 95%. Each koji strain has a unique character. Therefore, the company selects the strains that meet each client’s request and decides upon their blend ratio accordingly.

Nowadays, the company cultures seed koji in a clean environment in which bacteria are removed by air filters and other means. Defending against bacteria was a very stressful task in the past, when such devices were not available.

One secret method passed down through the generations at Hishiroku is adding wood ash to koji mold. Creating an alkaline environment inhibits the reproduction of harmful microorganisms.

Additionally, phosphoric acid and potassium contained in wood ash encourage the growth of koji mold, and trace metals, such as copper and zinc, promote the settlement of koji spores.

There are also secret techniques for choosing and mixing different types of wood ash. Some people would say things like, “The ash from burned camellia trees in Kyoto’s Ohara district should be good.”

It is not clear when people started using koji mold to make sake.

According to Harushi Nakajima, a Meiji University professor in applied microbiology, sake was made with human saliva in ancient times. When a person puts rice in their mouth and chews it, amylase, an enzyme in saliva, changes starch into sugar. When the person spits out the rice and lets it stand, natural yeast gets into the rice from outside and produces alcohol from the sugar. Such sake is called kuchikamizake (mouth-chewing sake).

After kuchikamizake came “mold sake,” which was made with koji mold. An ancient document from the early eighth century, called “Harima-no-kuni Fudoki” (Records of local customs and climate in Harima) — Harima was located in what is now Hyogo Prefecture — introduces a method to make sake using mold from growing koji mold on rice. Amylase produced by koji mold breaks down starch.

Unlike kuchikamizake, this method made mass production of this type of sake possible. The sorting of koji mold also began in order to produce even better sake.

First pure culture of koji mold

During the Muromachi period, there was already a group called Koji-za, which consisted of expert koji growers and provided sake breweries with quality koji mold. At first, they increased their quantity of koji by taking steamed rice on which the mold was growing and mixing it with more steamed rice. However, a technique for culturing only the desired strain was soon developed, and a seed koji shop selling koji spores was set up.

German bacteriologist Robert Koch, who developed a method to culture bacteria on agar in the 1870s, is commonly said to be the first person in the world to grow microorganisms based on pure culturing. However, history shows that pure culturing was effectively developed much earlier in Japan.

“We can call it the world’s first pure culturing of a microorganism. It’s astounding,” Nakajima said.

“Seed koji shops can be called the world’s oldest bio-business,” said Katsuhiko Kitamoto, a professor emeritus in applied microbiology at the University of Tokyo.

Since it is a business, competition among different seed koji makers has arisen.

“They ask sake brewing companies, which are their clients, about what kind of sake they have made from the koji mold they sold, to make the most of the information on selecting the right strain,” Kitamoto said. “Years of such experience has led to the production of good-quality sake.”

‘Domesticated’ nature

Genome studies have revealed that Aspergillus oryzae, or koji mold, is more suited to the fermentation industry than naturally occurring molds. Apparently, this may be regarded as the result of people having domesticated koji mold so that it became easier for them to use it.

Koji mold has about 12,000 genes in eight chromosomes. A similar species, Aspergillus flavus, has a gene for producing a toxin by the name of aflatoxin. Koji mold does not produce this toxin, indicating that it either does not have the gene or that the gene is inactive.

Also, Aspergillus flavus has only one gene of alpha-amylase, an enzyme that breaks down starch, while koji mold has three genes of this type, meaning that it has a greater capability to produce sugar.

One interesting item to note is that Aspergillus flavus produces spores in bright places, whereas koji mold does so in dark places. It is believed that koji mold’s preference when producing spores changed from bright places to dark places because koji seed is produced in the dark in a koji-muro (koji chamber).

In 2005, a research team consisting of members of the National Institute of Advanced Industrial Science and Technology and other institutes announced the sequencing of the koji mold genome. The team was led by Masayuki Machida, now a professor at the Kanazawa Institute of Technology specializing in genomic science.

“Seed koji shops have been culturing koji mold for many years. Over the course of time, the genes of koij mold are believed to have changed as well,” Machida said. “Indeed, we can say that Japanese people and koji mold have developed fermented food and the koji mold industry together.”