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Fermented Foods: Types, Examples, and Health Benefits

A guide to fermented foods: the main types (dairy, soybean, vegetable, beverages), the microbes behind each, and the health benefits of fermentation.

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Aastha Shrestha
Aastha Shrestha is a Biotechnology graduate with an M.Sc. from National College, Tribhuvan University. Her academic interests center on Molecular Biology and Immunology; two fields that are increasingly converging in modern diagnostic and clinical microbiology.
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The word fermentation comes from the Latin verb fervere, meaning "to boil," after the bubbling that appears when sugars are fermented. It is one of the oldest ways to preserve and transform food, using the metabolic activity of microorganisms.

Fermented foods are foods and beverages produced by the controlled activity of microorganisms, which change the food's flavor, texture, aroma, and color, and often extend its shelf life. They are made all over the world, and most fall into a few clear groups based on the raw material and the microbes involved: fermented dairy, fermented soybean products, fermented vegetables, and fermented beverages. This article walks through each group.

Advantages of Fermented foods

Traditionally, the foods were fermented to prevent spoilage and preserve for an extended period. Some of the few advantages of fermenting foods are given below.

  1. It preserves the foods and is economical; for example, cheese prepared from milk can be preserved for longer than the source.
  2. It also removes the unwanted or harmful properties of raw materials.
  3. The presence of microorganisms enhances the nutritional content of food.
  4. In comparison to raw materials, the organoleptic properties of fermented foods are improved due to fermentation.

How fermented foods are grouped

Although hundreds of fermented foods exist, most can be understood by asking two questions: what is the raw material, and what microbe does the fermenting? The answers sort nearly all fermented foods into four families, and the microbe usually explains the food's character.

Food Raw material Main microbe(s) Type of fermentation
Yogurt Milk Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus Lactic acid (bacterial)
Cheese Milk Lactic acid bacteria; molds in some types Lactic acid (bacterial)
Kefir Milk Mixed bacteria and yeasts (kefir grains) Lactic acid + alcoholic
Soy sauce Soybean, wheat Aspergillus oryzae, then yeasts and bacteria Mold + brine (bacterial/yeast)
Miso Soybean, rice/barley Aspergillus oryzae (koji), yeasts, LAB Mold + brine (bacterial/yeast)
Tempeh Soybean Rhizopus oligosporus (mold) Mold
Natto Soybean Bacillus subtilis (natto) Bacterial
Sauerkraut Cabbage Leuconostoc, Lactobacillus Lactic acid (bacterial)
Kimchi Cabbage, radish Leuconostoc, Lactobacillus, Weissella Lactic acid (bacterial)
Beer / wine Cereals / grapes Saccharomyces yeasts Alcoholic

Two patterns are worth noticing. Vegetable and dairy ferments are mostly the work of lactic acid bacteria, which produce acid that both preserves and sours the food. Soybean ferments are more varied: some use molds (tempeh, the koji step of miso and soy sauce), while natto stands out as the one made by a bacterium, Bacillus subtilis. Beverages are the domain of yeasts, which make alcohol.

Traditional Fermented Foods

Fermented foods can be produced from raw materials such as milk, soybean, cabbage, fruits, etc. Other organisms, such as Lactobacillus, ferment these raw materials. Some of the foods produced from these raw materials are mentioned below:

Fermented Milk Products

Milk is used as raw materials for producing foods such as yogurt, curd, kefir, cheese, probiotic drinks, etc.

Yogurt: Yogurt is a popular dairy product made from milk fermented by two bacteria working together, Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus. In addition, a few other organisms act as starter cultures: Bifidobacterium spp., Lactobacillus delbrueckii, Lactobacillus casei, and Lactococcus lactis, among others. These bacteria ferment milk and produce lactic acid, which drops the milk pH from 7 to 4-5, which coagulates it. Produced lactic acid causes the sour taste of yogurt and inhibits the growth of spoilage bacteria.

Yogurt - YogurtFigure: Yogurt

Fermented Food from Soybeans

Soybean is a nutritional food rich in protein (42%), oil (18%), and low carbohydrates (17%). The bean consists of phospholipids, nucleic acids, and vitamins such as thiamine, riboflavin, and niacin. (2) Even though it is nutritious, some compounds cannot be digested, which, after fermentation, are reduced to a lower molecular weight and are made digestible. Some fermented soybean products include Soy sauce, Miso, Tempeh, Natto, etc.

Soy sauce

Soy sauce, known in Japan as shoyu, is a deep red-brown liquid with a salty taste and distinct aroma. Its main raw materials are soybean and wheat, fermented with salt and a mixture of the koji mold Aspergillus oryzae followed by yeasts and bacteria during a long brine fermentation.

Natto

Natto originated in Japan over 1,000 years ago. The familiar natto, itohiki-natto, is whole soybeans fermented by the bacterium Bacillus subtilis (natto). This is what makes natto distinctive: it is the one major soybean ferment made by a bacterium rather than a mold, and the bacterium produces the sticky, stringy threads and strong aroma natto is known for. (A separate, less common salted product called hama-natto is made with the mold Aspergillus, but it is a different food from the sticky natto most people mean.)

Natto - NattoFigure: Natto

Tempeh is popular in Indonesia and eaten as an important protein source. Several species of Rhizopus are used to ferment the soybean, mainly Rhizopus oligosporus. The mold binds the cooked beans into a firm cake with a mild, nutty flavor.

- TempehFigure: Tempeh

Miso

Miso is a fermented soybean paste that is popular in Japan. Soybean is mainly used as a substrate for miso production; other legumes such as chickpeas or novel bases like nuts may also be used. Miso is made with koji, a culture of the mold Aspergillus oryzae grown on rice or barley. The koji is then combined with cooked soybeans, salt, and salt-tolerant yeasts and lactic acid bacteria, which carry out a slow second fermentation. Miso production therefore has two fermentation steps.

The mixture is then aged, sometimes for months or years, which develops miso's deep flavor before it is packaged.

Miso - MisoFigure: Miso

Fermented Food from Vegetables

Vegetables such as cabbages, olives, cucumber, onions, peppers, green tomatoes, carrots, okra, celery, and cauliflower can be fermented and traditionally have been used as a means to preserve. Some fermented vegetables are kimchi, sauerkraut, olives, pickles, and mustard pickles.

Kimchi

Kimchi is a fermented vegetable dish that originated in Korea. The main ingredients are Chinese cabbage or radishes and flavoring ingredients such as chili, pepper, garlic, onion, ginger, and seasonings such as salt, soybean sauce, sesame seed, and other additional foods such as carrot, apple, pear, and shrimp. All these ingredients are mixed, and the fermentation occurs naturally by microorganisms in the cabbage or other elements. Although fermentation occurs naturally, for the commercial production of kimchi, lactic acid bacteria are the key fermenters, mainly Leuconostoc, Lactobacillus, and Weissella. But the concentration of bacteria differs in different stages of fermentation; bacteria belonging to Leuconostoc genera dominate the first three days of fermentation. Since various ingredients are added to kimchi, the composition of microbes may vary accordingly.

For example, after red pepper powder is added, Weissella can become more abundant while Leuconostoc and Lactobacillus decrease.

- KimchiFigure: Kimchi

Sauerkraut

It originated in the 4th century and is a common form of preserving cabbage. It is popular in Germany and is now common in other European, Asian countries, and the United States. The raw materials are cabbage and salt (about 2.3 to 3.0%), fermented spontaneously. The organisms that carry out the fermentation are Leuconostoc spp., Lactobacillus spp., and Pediococcus spp.

Cucumber (pickling) is eaten raw after fermentation or pickling. Dry salting and brine salting are widely used. During brine salting, salt is added in 5-8% amounts. The salt suppresses unwanted bacteria, allowing lactic acid bacteria and yeasts to grow during the primary fermentation, which lasts 2 to 3 days. The main fermenting organisms are Lactobacillus plantarum and L. brevis, followed by Pediococcus.

Fermented Beverages

Fermented beverages are in either alcoholic form or stimulant form. Beer and wines are alcoholic drinks, while tea, coffee, and cocoa are stimulant beverages.

Alcoholic beverages

Alcoholic beverages are famous worldwide and are being produced in different societies. It is mainly based on the conversion of sugar to alcohol by yeasts. The primary organism involved in the fermentation of alcohol is yeasts, and the raw material used in most distilled liquors are honey, sugarcane, palm sap, beetroot, maize, or corn. The main brewing and wine yeast is Saccharomyces cerevisiae, with different strains giving different products.

Wine

In the case of wine, historically, the fermentation of grape species called Vitis vinifera produces wine. When a grape is ripe, its moderate acidity is favorable to make wine. Its natural sugar content acts as a raw ferment material and can produce wine with 10% or higher alcohol. It contains tannins that provide flavor and protect wines from spoilage bacteria. Other fruits such as guava, mangoes, pineapple, tangerine, cashew fruit, and many more contain 10-20 % fermentable sugar, which can be used to produce wine. Still, the names of fruits included papaya wine, guava wine, and so on.

Beer

It is a beverage, is obtained by the fermentation of malted cereals. Malted cereal is extracted with water and other carbohydrates. This extract is boiled with hops and later cooled and fermented with yeast. Fermentation of cereal extracts by Saccharomyces is a crucial step involved during brewing. Even though all Saccharomyces strains produce ethanol, the type of strain used determines the production of beers and is classified as lager or ale beers. (6)

Lager beer is bottom-fermented, using Saccharomyces pastorianus (historically called S. carlsbergensis), the bottom-fermenting yeast.

Ale beer is top-fermented, using Saccharomyces cerevisiae, the top-fermenting yeast.

Beer in Gravity tap - BeerFigure: Beer

In addition, there are distilled beverages such as whiskey, rum, brandy, etc. Whiskey, rum, and Brandy are obtained by distillation of aqueous extract of infusion of malted barley or other cereals, the fermented juice of cane syrup or sugarcane derivates, and fermented grape, apple, pear, wine, and so on, respectively.

Stimulant beverages

Stimulant beverages such as tea, coffee, and cocoa are mainly produced in the rainforest zones of the Indian sub-continent, South America, and West Africa, respectively. A few stimulant beverages are discussed below.

In the case of coffee fermentation, it originated in Ethiopia. The microorganisms used in fermentation include spore-forming and non-spore-forming bacteria. In addition, other lactic acid bacteria (Leuconostoc spp and Lactobacillus spp) and yeasts (Saccharomyces spp and Schizosaccharomyces spp.) are also used. Processing of coffee involves two methods: the wet method and the dry method.

While using the wet method, fruits are passed through a pulping machine to remove the pulp, and pectinolytic enzymes produced by microorganisms remove the mucilage. On the other hand, while using the dry method, fruits are dehulled to remove dry outer portions. The coffee may also be dried by exposing it to the sunlight.

Coffee beans (unroasted) - Coffee beansFigure: Coffee beans

The tea was originated in South-East China and is now popular worldwide. Young tea leaves are handpicked and withered. Leaves are squeezed to extract juices by rolling, which is further spread on the surface of the leaves.

The juice contains polyphenols that are exposed to oxygen and oxidize, turning the leaves from green to brown. Note that this step is traditionally called "fermentation" in the tea industry, but it is mostly enzymatic oxidation by the leaf's own enzymes, not true microbial fermentation. The leaves are then dried with hot air at about 80 to 90°C, sorted, and graded.

Dried tea leaves - Dried tea leavesFigure: Dried tea leaves

Cocoa is native to South America but is now produced in Ghana, Ivory Coast, Cameroon, Malaysia, and Nigeria. The tree grows a pod consisting of 40-60 seeds. The mucilaginous outer covers of sources are broken.

They are left to ferment by a succession of microbes (yeasts, then lactic acid bacteria, then acetic acid bacteria), which changes the seed color from pale to brown and develops the compounds that give chocolate its aroma.

Cocoa pods - Cocoa podsFigure: Cocoa pods

Health Benefits of Fermented Foods

Fermented foods have a long history of safe use and are accepted widely by the public owing to their favorable health effects. The positive impacts of these have attracted consumers in large numbers.

  1. Fermented food consumption can positively affect mood, brain activity, and gut microbes. Regular yogurt consumption has been associated with a lower risk of cardiovascular disease and type-2 diabetes in observational studies. Intake of kimchi is linked to anti-diabetic and anti-obesity effects.
  2. Fermentation transforms the raw materials allowing the food to be tolerated by consumers. This process improves the digestibility of starch and polypeptides by breaking them down into oligosaccharides and amino acids. For instance, the casein micelle of milk is destabilized by the fermentation of bacteria present in the milk, enhancing the digestibility of milk protein. Fermentation can also generate bioactive compounds from proteins, fats, and carbohydrates. Studies have associated these with benefits such as lower blood pressure and cholesterol and effects on immune function, though the strength of evidence varies by food and by study. Some fermented dairy products also contain B vitamins such as folate (B9) and B12.
  3. Microorganisms such as Zymomonas, Leuconostoc, Pediococcus, and Streptococcus species and other members of the Lactobacillaceae family produce exopolysaccharides. These organisms have high molecular weight exopolysaccharides from simple sugars found in raw materials. EPS-producing LAB helps in immunomodulation which depending on factors, may be suppressive or stimulatory.
  4. Fermented food modulates the gut microbiome. For example, wine is rich in polyphenols, alters gut microbiota, and lowers total cholesterol and blood pressure. It also inhibits pathogenic bacteria and benefits the beneficial bacteria.

How to Remember

Four families, sorted by raw material.
Dairy (milk), soybean, vegetable, beverage. Name the raw material and you are most of the way to the food. Milk gives yogurt and cheese; soybean gives soy sauce, miso, tempeh, natto; cabbage gives sauerkraut and kimchi; grapes and grain give wine and beer.

The microbe explains the food.
Lactic acid bacteria sour dairy and vegetables. Molds handle most soybean ferments (tempeh, and the koji step of miso and soy sauce). Yeasts make alcohol. And one oddball: natto is the bacterial soybean ferment (Bacillus subtilis).

Natto is the bacterial one.
Among soybean ferments, tempeh and miso use molds, but natto uses a bacterium, Bacillus subtilis. That bacterium makes the famous sticky threads. If a question asks which soybean ferment is bacterial, it is natto.

Beer's two families: top and bottom.
Ale is top-fermented (Saccharomyces cerevisiae); lager is bottom-fermented (Saccharomyces pastorianus, historically called S. carlsbergensis). Ale rises, lager sinks.

Key exam facts in one table

Point High-yield fact
Definition Food transformed by controlled microbial activity, changing flavor, texture, and shelf life
Four groups Fermented dairy, soybean, vegetable, and beverages
Yogurt organisms Streptococcus thermophilus + Lactobacillus delbrueckii subsp. bulgaricus
Tempeh organism Rhizopus oligosporus (mold)
Natto organism Bacillus subtilis (bacterium; the one bacterial soybean ferment)
Miso / soy sauce key organism Aspergillus oryzae (koji mold)
Sauerkraut / kimchi organisms Leuconostoc, Lactobacillus (LAB)
Kimchi early dominant genus Leuconostoc (first few days)
Wine grape Vitis vinifera
Ale vs lager Ale = top-fermenting S. cerevisiae; lager = bottom-fermenting S. pastorianus
Tea "fermentation" Actually enzymatic oxidation, not microbial
Main preservation mechanism Acid or alcohol produced by microbes inhibits spoilage organisms

Where Students Get Confused

Which soybean ferment is made by a bacterium, not a mold?
Natto. It is fermented by Bacillus subtilis, which produces its sticky threads. Tempeh uses the mold Rhizopus, and miso and soy sauce use the mold Aspergillus oryzae (koji). Natto is the bacterial exception.

Is tea really fermented?
Not in the microbial sense. What the tea industry calls "fermentation" is mostly the leaf's own enzymes oxidizing polyphenols after the leaves are bruised. True fermentation, as in yogurt or beer, is done by microbes. Tea is a common trick question for this reason.

What is koji?
Koji is not a food itself but a starter: the mold Aspergillus oryzae grown on steamed rice, barley, or soybeans. It supplies the enzymes that break down starch and protein, and it is the first step in making miso, soy sauce, and sake.

Why does yogurt need two bacteria?
Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus work as a pair, each stimulating the other's growth (a relationship called protocooperation). Together they acidify the milk faster and produce yogurt's characteristic flavor and texture.

Do fermented foods spoil?
Fermentation greatly extends shelf life because the acid or alcohol produced blocks spoilage microbes, but it does not make food last forever. Fermented foods can still spoil eventually, especially once opened or if contaminated.

References

  1. Terefe NS. Food fermentation. In: Reference Module in Food Science. Elsevier; 2016. https://doi.org/10.1016/B978-0-08-100596-5.03420-X
  2. Sharma R, Garg P, Kumar P, Bhatia SK, Kulshrestha S. Microbial fermentation and its role in quality improvement of fermented foods. Fermentation. 2020;6(4):106.
  3. Okafor N. Modern Industrial Microbiology and Biotechnology. Enfield (NH): Science Publishers; 2007.
  4. Allwood JG, Wakeling LT, Bean DC. Fermentation and the microbial community of Japanese koji and miso: a review. J Food Sci. 2021;86(6):2194–2207.
  5. Dimidi E, Cox SR, Rossi M, Whelan K. Fermented foods: definitions and characteristics, impact on the gut microbiota and effects on gastrointestinal health and disease. Nutrients. 2019;11(8):1806.
  6. Bokulich NA, Bamforth CW. The microbiology of malting and brewing. Microbiol Mol Biol Rev. 2013;77(2):157–172.
  7. Heinen E, Ahnen RT, Slavin J. Fermented foods and the gut microbiome. Nutr Today. 2020;55(4):163–167.
FAQ

Frequently Asked Questions

What are fermented foods?

Fermented foods are foods and drinks transformed by the controlled activity of microorganisms such as bacteria, yeasts, and molds. The microbes change the food's flavor, texture, and aroma, and often help preserve it. Examples include yogurt, cheese, kimchi, sauerkraut, tempeh, miso, beer, and wine.

What are the main types of fermented foods?

They fall into four broad groups: fermented dairy (yogurt, cheese, kefir), fermented soybean products (soy sauce, miso, tempeh, natto), fermented vegetables (kimchi, sauerkraut, pickles), and fermented beverages (beer, wine, and others).

Which microbes are used to make fermented foods?

It depends on the food. Lactic acid bacteria make yogurt, cheese, sauerkraut, and kimchi. Molds like Aspergillus oryzae and Rhizopus make miso, soy sauce, and tempeh. Yeasts like Saccharomyces cerevisiae make beer and wine. Natto is unusual, made by the bacterium Bacillus subtilis.

How does fermentation preserve food?

The microbes produce acids (like lactic acid) or alcohol, which lower the pH or create conditions that stop spoilage and disease-causing microbes from growing. This is why fermented foods last longer than the raw ingredients they are made from.

Are fermented foods good for health?

Many fermented foods are associated with benefits such as improved digestion, a healthier gut microbiome, and better nutrient availability. Some contain probiotics. Benefits vary by food, and fermented foods can be high in salt, so they are best eaten as part of a balanced diet.

Is natto made by a mold like tempeh?

No. Natto is made by the bacterium Bacillus subtilis, which gives it its sticky, stringy texture. Tempeh is made by the mold Rhizopus. This is a common point of confusion because both are fermented soybean foods.

Is tea a fermented food?

Not in the true sense. What is called "fermentation" in tea processing is mostly enzymatic oxidation by the leaf's own enzymes, not fermentation by microbes. True fermented foods, like yogurt and beer, are transformed by living microorganisms.

Acharya Tankeshwar
About Reviewer
Acharya Tankeshwar

Tankeshwar Acharya, MSc (Medical Microbiology)

Tankeshwar Acharya is an Assistant Professor in the Department of Microbiology at Patan Academy of Health Sciences (PAHS), Nepal, where he has been teaching and practicing clinical microbiology for over 14 years. He is the founder of Microbe Online, one of the leading free microbiology education resources on the web, covering bacteriology, mycology, parasitology, immunology, and clinical laboratory diagnostics written from direct experience in both the classroom and the diagnostic laboratory.

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