How Fermentation Works to Preserve Food and Punch Up Flavors

Takashi Sato

February 26, 2023
In the manufacturing process of fermented foods, amino acids are released in the process of decomposing proteins contained in foodstuffs in order for microorganisms to secure their own nutrients, resulting in unique flavors. The mixture of amino acids produced by aging proteins generally gives off a sense of umami. Umami and sweetness enhance the taste of food, and sourness and bitterness also contribute to richness and flavor.

Since people don’t hibernate, we need to feed ourselves every day. In the past, this meant contending with harsh winters where food was less readily available. Even today, certain items are only available in particular seasons. Prehistoric humans needed to think long and hard about procuring food. Some, in times of desperation, probably even resorted to eating less-than-fresh foods that may have given off unpleasant odors. It was a game of trial and error at the time, with losers falling ill. The winners, though, were perhaps unknowingly taking the first steps onto the path toward fermented foods as we know them.

As fermentation geeks probably know, preventing food from spoiling means inhibiting the growth of bad bacteria that can cause food poisoning. Controlling bacteria means striking the right balance between temperature, moisture, salt content and pH levels.


In the fresh fish section of many grocery stores, one might find the section is further separated into fish for raw consumption, and fish that needs to be cooked – even among the same type of seafoods. You may find oysters, for example, ready for raw consumption, with other oysters just a few feet away that need to be cooked. For seafood meant to be cooked, the cooking process most often kills any unwanted bacteria. We may have the folks of our ancient past to thank for this, who discovered that fire can render less-than-fresh meats safe.
On the other hand, refrigeration can also slow or prevent spoilage. Refrigerators are purpose-built to prevent bad bacteria from growing, at least for a while. Electric refrigerators may be a fairly new invention in the grand timeline, but ancient peoples most likely used ice chambers to achieve similar results without electricity.


Drying was probably the first method invented for preserving food. Ancient people would have dried fish caught in abundance by laying the fish not immediately needed in the sun. Smoking was also deployed on game meats remove the moisture, thereby securing food for later use. Fruits with small grains, like grapes, could be dried and preserved, too. Certain grains with low moisture content could also be preserved.
There are also a number of fermented foods that are preserved by drying, like the Japanese staples of dried bonito flakes and dried fermented soybeans.

Salt content

The salinity of seawater is about 3.5%, but when the salinity reaches about 8%, the number of microorganisms that can reproduce is drastically reduced, and when it exceeds 15%, most microorganisms simply can’t grow at all. This is because osmotic pressure sucks out the water in the cells of organisms. Since ancient times, humans have preserved foods like fish, animal meat and vegetables, which are prone to spoilage, by preserving them in salt. Even today, fish and shellfish are preserved by salting, and animal meat is processed into ham, corned beef, and other products with longer shelf lives. There are, in fact, halophilic bacteria that can grow in the presence of high concentrations of salt. But these microorganisms are slow-growing and require high concentrations of salt, so they’re typically not a worry for people.
Many fermented foods, like soy sauce and miso, are preserved by their high concentrations of salt.


If vegetables like Chinese cabbage are left to rot, they will turn to mush, but if they are placed in a jar and soaked in rice bran, they will soon develop a tangy flavor and last longer. Thus, when foods containing sugar are stored with limited aeration, lactic acid bacteria often begin to proliferate. Lactobacilli produce large amounts of lactic acid to lower the pH, or acidity, thereby killing germs that prefer a pH near neutral and creating a favorable environment for themselves. Since most putrefactive bacteria and pathogenic bacteria prefer a neutral to slightly basic environment, when lactobacilli grow and the pH drops to about 4.3, few potentially dangerous organisms can thrive.
Lactobacilli play a very important role in the production of fermented foods. It is easy to imagine lactobacilli working as the main ingredient in pickles and yogurt, but lactobacilli also play an important role in the production of cheese, sake, flavorings, soy sauce and red wine.
Vegetables and fruits contain large amounts of sugar. Starch, the main component of grains, also becomes sugar when it decomposes. Starch and sugars are composed of carbon (element symbol C), hydrogen (H), and oxygen (0), each in the ratio of 1 :2 : 1. In other words, carbon (C) is combined with water (H2O) and this becomes the well-known carbohydrate. When decomposed by microorganisms, sugars produce organic acids such as lactic acid and acetic acid, which lower the pH. This results in a sweet and sour aroma and a strong acidic flavor.
On the other hand, fish, animal meat, and milk contain large amounts of protein. Proteins contain nitrogen (N) and sulfur (S) in addition to carbon, hydrogen, and oxygen, so when decomposed by microorganisms, nitrogen-containing amines and ammonia proliferate, causing the pH to rise. In addition to taking on a strong aroma due to the formation of nitrogen- and sulfur-containing compounds, it is extremely dangerous because the pH tends from neutral to basic, making it easy for putrefactive bacteria and pathogens to grow. In such fermented foods, the growth of pathogens is often prevented by adding large amounts of salt.
Pickling is an effective way to preserve vegetables for a long time, but to prevent spoilage, a large amount of salt is added or enough lactic acid bacteria are grown to make the environment acidic at a pH of about 4. Salty or sour pickles made in this way can be stored at room temperature for a long time. On the other hand, Japanese “asazuke” pickles do not meet these conditions and are prone to spoilage. This is the reason why asazuke requires refrigeration and must be eaten as soon as possible.

Fermentation means flavor

Even the finest beef isn’t what most would consider “tasty” immediately after butchering. It’s only after it undergoes a maturing process known as aging that it becomes something special. In the common wet aging method, a block or half carcass of beef is vacuum-packed and stored at temperatures near 0°c (32°f) for 20-25 days. Chilled beef imported from North America and Oceania take 3 to 5 weeks for transportation and distribution, so by the time it arrives in, say, Japan, the aging process is complete and the beef is ready to eat. During the aging period, due to proteolytic enzymes in the meat, the fibers of the meat slowly break down and become tender, and amino acids are released to bring out the flavor.
In general, protein doesn’t actually taste like much. Think of almost pure protein components such as the egg itself, tofu, or chicken breast. Proteins are composed of a large number of amino acids linked together, and amino acids themselves do have flavor. For example, the sodium salt of glutamic acid, one of the most abundant amino acids, is a flavor enhancer itself. Each of the 20 amino acids that make up proteins have their own unique flavor. Generally speaking, hydrophilic amino acids that dissolve easily in water, such as glycine, have a sweet flavor, while acidic amino acids like glutamic acid have a umami or sour flavor. On the other hand, basic amino acids like arginine and hydrophobic amino acids that are less soluble in water, such as phenylalanine, often have a bitter flavor.
In the manufacturing process of fermented foods, amino acids are released in the process of decomposing proteins contained in foodstuffs in order for microorganisms to secure their own nutrients, resulting in unique flavors. The mixture of amino acids produced by aging proteins generally gives off a sense of umami. Umami and sweetness enhance the taste of food, and sourness and bitterness also contribute to richness and flavor. This fermentation mechanism brings out umami, that much-beloved flavor that’s hard to describe but all-too-important for great-tasting cuisine.

Source: 『Nihon no dento. Hakko no Kagaku. Biseibutsu ga Umidasu Umasa no himitsu』Harushi Nakajima

President at San-J International | + posts

Takashi Sato, founder of Hakko Hub and President of San-J International, is an 8th generation soy sauce brewer. With a passion for excellence, he has elevated tamari soy sauce production to new heights. Dedicated to tradition and innovation, Takashi is shaping the future of fermented foods.