A primer on the biochemistry of miso and soy sauce fermentation

This article sets out to explain what happens to miso and soy sauce when fermenting, i.e. the basic biochemical mechanisms that happen during that time. Don’t be put off by the word biochemistry, you’ll see it’s quite simple! :)

Often when I talk about koji, koji spores, miso, soy sauce, the role of koji in the whole process, I often find that my friends and family members are getting a bit confused, so I figured to do a little write-up of the whole thing.

Where to start? Most people know soy sauce and a few know miso, though the latter mostly in the form of miso soup.

Miso is a fermented paste which consists of usually rice koji, mashed cooked soy beans and a good amount of salt. Every ingredient is vital in its own way, but koji is the most vital.


Koji is the japanese name for Aspergillus oryzae. It is a fungus that is traditionally grown on rice, barley or on soy beans. It produces manyfold enzymes, which are needed to make miso and soy sauce.

A lot of confusion arises from the fact that koji is the name for both the fungus and for the substrate (rice, barley, soy, etc.) on which the fungus has been grown on. The latter usually carries the name of the substrate in front of it, i.e. rice koji or barley koji.

Koji Spores – basically the “seeds” of the fungus
Rice Koji – This is rice on which the fungus has been grown.

The basic biochemical mechanisms that are behind ferments involving koji

In some way, fungi are more similar to animals than to plants in their way of “feeding” themselves. Fungi, like animals, use organic matter to generate energy. In biological terms: they are heterotrophes (plants on the other hand are autotrophes, they generate organic matter from inorganic matter using sunlight).

When we create a batch of miso we make use of this fact. Because the fungus can’t just use the complex molecules that plants make (starches, proteins, cellulose, fats, etc.), the fungus has to produce enzymes to digest them. Enzymes are basically “worker molecules” that break down these macro molecules to usable molecules. This is very much analogous to what happens in our digestive tracts.

These enzymes are at the heart of ferments involving koji. There are enzymes that break down starches to sugars, a process that also makes possible the brewing of sake. Starch is basically a very long chain of glucose molecules that are connected. The enzyme amylase (all enzymes have an -ase suffix) severs those connections to yield single glucose molecules.

This is also what happens if you chew white bread for long enough: the amylases in the mouth break down the starch to yield glucose, thus the mush will start to taste sweet, try it! (if you haven’t already at some point in your life)

Actually it "hydrolyses" it. Every time a glucose molecule is cut off, one molecule of water is used.

(This is more an illustration of principle rather than actuality. The starch is not exclusively broken down only to glucose, but also to maltose (basically two connected glucose molecules) and to other dextrins (2-20 glucose molecules).)


Analogously, proteins are macro molecules made of amino acids. Unlike starch, which is made exclusively of glucose, proteins are made of 22 different kinds of amino acids.  Koji produces enzymes to break down these proteins to amino acids.

Protease breaking down a protein – basically a chain of amino acids – into its constituent parts

Why miso and soy sauce taste the way they do

So Koji is grown in order to get a substrate with lots of enzymes in it. (Well, and also because it tastes amazing) The enzymes are then let loose on whatever the miso is made with, traditionally soy beans.

Soy bean protein by itself tastes very dull (in my humble opinion), but if enzymes break that protein down into its constituent amino acids, the taste changes from dull to delicious, imparting an umami taste.

This is because the soy protein contains a lot of glutamate, the salt of which you might know as MSG – mono sodium glutatmate. Many people get an “oh but MSG is bad” reflex, but in my opinion the problem with MSG is not the MSG itself, but the fact that it is mostly used by industrial food producers and cheap restaurants to mask the low quality of their foods.

The umami of MSG is very one-dimensional, while the umami of miso is very much multi-dimensional due to the multitude of different amino acids and fermentation products. It’s not a single compound, miso consists of a huge array of different compounds that create a depth of taste that a single isolated compound just can’t. It would be wrong to reduce the magic of miso fermentation to glutamate, since there are so many things going on.

The function of salt and salt tolerant microbes

Another very important ingredient is salt. Without salt the result after a few months of fermentation would not be miso, it would be compost. Salt inhibits many unwanted microbes. Actually the koji fungus does not tolerate the levels of salt required for making miso. So once the miso is mixed, the fungus dies but its enzymes (which are salt tolerant) remain.

Some microbes do tolerate these levels of salt (in a miso that’s about 8-13%), for example lactobacilli and some yeasts. The former produce lactic acid (which lowers pH) and other compounds that add to the characteristic taste of miso. Salt-tolerant yeasts produce alcohol and other compounds that add to taste. The alcohol too is turned into other compounds.

It is possible to make soy sauce on the fast track. Some producers do that by chemically breaking down these macro molecules, i.e. proteins and starches, by boiling them with hydrochloric acid.  This process misses the long ageing and the additional microbes described above that make miso and soy sauce to the wonderful foods that they are. The producers know that and make up for it by using aromas, coloring agents and whatnot.

These fast-track sauces always fall short in blind tasting tests. So the message is clear: long term fermentation is the noble path to deliciousness!


If you have questions or if you found some fault with my explanation, please let me know. Thanks for reading!