36 Microbial Fermentation Examples in Real Life


For many, fermentation simply means spoilage of food or alcohol production. Although the latter is correct, fermentation is far from food spoilage and it rather prevents it. In a more general sense, fermentation is a deliberate process intended to get the desired results. Fermentation is the substantial growth of microorganisms on their suitable growth medium. It is a natural metabolic process in which microorganisms convert carbohydrates (sugar) into alcohol, gases, or acid. The primary biochemical role of fermentation includes energy production in anaerobic conditions. When induced via industrial fermentation, it pursues the aim of producing more specific chemical products like food additives, antibiotics, enzymes, vaccines, etc.

Did you know? The scientific study of fermentation is known as zymology. It was discovered by the renowned French microbiologist Louis Pasteur in 1857.

Types of Fermentation

During the process of fermentation, pyruvate undergoes metabolic transformations, leading to the formation of various compounds. This intricate process can be categorized into different types:

1. Ethanol Fermentation

Also known as alcoholic fermentation, this pathway involves the production of ethanol and carbon dioxide.

2. Lactic Acid Fermentation

Lactic acid fermentation encompasses two distinct methods of lactic acid production:

a. Homolactic Fermentation

This type exclusively produces lactic acid in the presence of homolactic LAB (lactic acid bacteria), such as Lactococcus, Enterococcus, Streptococcus, Pediococcus, and the group I lactobacilli spp.

b. Heterolactic Fermentation

Unlike homolactic fermentation, heterolactic fermentation results in the production of lactic acid along with other acids and alcohols. Heterolactic bacteria, including Leuconostoc, Oenococcus, Weissella, and group III lactobacilli spp., are responsible for this process.

3. Facultative Fermentation

Certain members of the Lactobacillus genus possess the ability to perform aerobic respiration, making them facultative anaerobes. This sets them apart from other members of the order, which are all aerotolerant. The utilization of oxygen enables these bacteria to cope with stress. Lactobacillus spp. are responsible for this fermentation.

Microorganisms used in industrial fermentation

Fermentative Bacteria

Bacteria used in Industrial fermentation

Fermentative Fungi

Yeast and mold used in industrial fermentation


Fermented milk products

Fermented milk products – cheese, yogurt, sour cream, buttermilk, etc.

1. Yogurt


Yogurt fermentation process

The most widely used fermented milk product yogurt or curd is made by introducing specific strains of bacteria, such as Lactobacillus bulgaricus and Streptococcus thermophilus, into milk. These bacteria ferment the lactose, creating the characteristic tangy flavour and creamy texture of yogurt.

2. Kefir

Kefir fermentation

Kefir fermentation

Kefir is a cultured dairy product that originates from the Caucasus region. It is made by fermenting milk with kefir grains. Kefir has a unique effervescent quality and a slightly tangy taste. Like yogurt, kefir is rich in probiotics and offers potential digestive and immune system benefits.

3. Cheese

Cheese fermentation

Cheese fermentation

Various types of cheese are produced through fermentation and curdling of milk. Different bacterial cultures and enzymes are used to coagulate milk proteins, separating the curds from the whey. The curds are then pressed and aged to develop a wide array of textures and flavours. Cheese is a versatile ingredient used in cooking, snacking, and as a topping.

4. Sour Cream

Sour cream fermentation

Sour cream fermentation

Sour cream is created by fermenting cream with lactic acid bacteria. The fermentation process thickens the cream and imparts a tangy flavour. Sour cream is often used as a topping for baked potatoes, tacos, and desserts.

5. Buttermilk

Buttermilk fermentation

Buttermilk fermentation

Traditionally, buttermilk was the liquid left over after churning butter from cream. Nowadays, cultured buttermilk is created by fermenting low-fat milk with bacteria. It is often used in baking to enhance the rise and tenderness of baked goods.

6. Labneh

Labneh fermentation

Labneh fermentation

Labneh (also known as leben or laban) is a Middle Eastern strained yogurt cheese made by straining yogurt to remove excess whey. The result is a creamy, tangy, and spreadable product that can be enjoyed as a dip, spread, or even in desserts.

7. Sauerkraut

Sauerkraut fermentation

Sauerkraut – made by fermenting cabbage in salt

Sauerkraut is a fermented cabbage dish made by massaging shredded cabbage with salt until it releases its juices. These juices create a brine that fosters the growth of lactic acid bacteria, which ferment the cabbage. The result is a tangy and crunchy condiment rich in vitamins, minerals, and probiotics. Some East-Asian traditional dishes such as kimchi, Suan cai, and Tsukemono are made with similar ingredients and fermentation methods.

8. Pickles

Pickling involves immersing vegetables in a brine solution of water, salt, and vinegar, or fermenting them in their juices. The natural sugars in vegetables are converted into lactic acid by beneficial bacteria. This process preserves the vegetables and imparts a sour and often crisp texture. Pickles offer a low-calorie, flavorful snack and serve as a great source of probiotics.

Fermented Vegetables

Fermented Vegetables – Kimchi, pickles, oil, etc.

9. Soy Sauce

Soy sauce fermentation

Soy sauce production as a result of koji (fermented soybean) and moromi (soybean mash) fermentation

Soy sauce is produced by fermenting soybeans and wheat with specific molds and yeast, often in combination with salt. The fermentation process, which can take several months to years, breaks down complex proteins and carbohydrates into savoury compounds. Soy sauce is a staple condiment in many cuisines and adds depth of flavour to a wide range of dishes.

10. Olives


Cured and packed olives

Olives are often consumed as snacks, appetizers, or used in cooking. Lactic acid bacteria naturally present in the olives initiate the fermentation process. The result is a product with a milder taste and unique aroma.

11. Oil

Fermented black garlic

Fermented black garlic is used in the making of black garlic oil

Some special oils, like black garlic oil, are made using a fermentation process. Black garlic, created by slow-cooking garlic bulbs at low temperatures over weeks, transforms the cloves into soft, dark, and sweet cloves. These cloves can then be infused into oil, producing a uniquely flavoured oil.

12. Wine

Wine is a classic product of fermenting grapes. The natural sugars in grapes are converted into alcohol by yeast during the fermentation process. This results in a diverse range of wines, including red wine, white wine, rose wine, sparkling wine, and dessert wine, each with a unique aroma and flavour.

Fermented fruits

Fermented fruits – red wine made from fermenting grapes

13. Vinegar

Vinegar fermentation

Vinegar fermentation

Vinegar is created through a two-step fermentation process. First, alcohol is produced from sugars in fruits, grains, or other fermentable materials. Then, acetic acid bacteria ferment the alcohol into acetic acid, giving vinegar its characteristic tangy taste. Vinegar serves as a versatile ingredient in cooking, dressing, and preservation.

14. Citric Acid

Citric acid

Citric acid

Citric acid is a natural acid found in citrus fruits like lemons, limes, and oranges. It is commonly used as a flavour enhancer, preservative, and acidity regulator in various food and beverage products. While it can be extracted from citrus fruits, it’s also produced through microbial fermentation of carbohydrates.

15. Tartaric Acid

Tartaric acid

Tartaric acid crystals production

Tartaric acid occurs naturally in grapes and is often used to enhance the tartness of foods and beverages. It’s a key component in cream of tartar, a byproduct of wine production, and is used in baking to stabilize egg whites and improve the texture of certain desserts.

16. Fumaric Acid

Fumaric acid

Fumaric acid production

Fumaric acid is found in various fruits and vegetables and is used as an acidulant in food and beverage products. It’s often employed in the production of powdered drink mixes, gelatin desserts, and candies.

17. Lactic Acid

Lactic acid fermentation

Lactic acid fermentation (LA is Lactic acid)

Lactic acid is produced by lactic acid bacteria during fermentation. It’s a common acidulant and preservative used in the food industry. Fermented foods like yogurt, sauerkraut, and pickles contain lactic acid, which contributes to their distinct flavours and acidity.

18. Starchy Plant Foods


Breadmaking, notice different stages of proofing due to fermentation

Starchy plant foods, such as cereals, roots, and tubers, play a significant role in human nutrition worldwide. Cereals are rich in carbohydrates, proteins, fibres, and vitamins necessary for the body’s energy production and growth. Similarly, roots and tubers are excellent sources of minerals like potassium, magnesium, and zinc. Besides their nutritional value as staples in many diets globally, these starchy plant foods have also been utilized in breadmaking through the process of microbial fermentation. This technique involves the use of microorganisms like yeast or bacteria to break down complex carbohydrates present in the flour into simpler sugars that can be easily metabolized during baking. Consequently, this innovative approach to breadmaking has gained popularity among professional bakers worldwide due to its positive impact on both product attributes and human health considerations. Beyond bread, fermentation is used to create a variety of products from grains. For instance, fermented rice products like idli and dosa in South Asian cuisine, as well as fermented maize-based foods and beverages in African cuisine, offer unique flavours and improved digestibility due to the fermentation process.

19. Seeds

Cocoa seeds

Fermented cocoa seeds are used in the making of chocolate

Fermented seed products such as soy products, nuts, chocolate, coffee, and oil made by microbial fermentation play a significant role in the food industry. Soybean oil derived from fermented soybean serve as a versatile protein source due to their high nutritional value and inclusion in various cuisines worldwide. Nuts are immensely popular for their antioxidant properties, healthy fats, and excellent flavour profiles. In addition to serving as indulgent snacks on their own, nuts are widely used in baking and cooking applications. Cocoa fermentation is the key step in chocolate making. Coffee derived from fermented coffee fruit is widely consumed for its aromatic taste. The oil obtained through microbial fermentation has gained attention for its sustainable production process, lower environmental impact compared to traditional methods, and potential health benefits due to the absence of chemicals or pesticides. Moreover, it provides a unique culinary experience with distinctive flavours that can enhance dishes across different cuisines. The incorporation of these oil seed products into professional food practices not only satisfies consumer demand but also promotes innovation and sustainability throughout the industry.

20. Fermented Sausages

Fermented sausages

Fermented sausages

Fermented sausages encompass a range of products like salami, pepperoni, and various regional specialities (French saucisson, Spanish chorizo, Italian salami, German salami, and Hungarian salami). These sausages are made by combining ground meat with spices, salt, and sometimes starter cultures containing beneficial bacteria. The fermentation process not only extends shelf life but also develops complex flavours and textures that are a hallmark of these cured meats.

21. Fermented Meat & Fish Products

In various cultures, fermented fish products such as whole salted fish, fish sauce, and fermented fish paste are prized for their unique flavours and preservation properties. Examples include cured whole fish such as buro (Philippines), pedah-kemburg (Thailand), and ngari(India); fermented fish paste such as ngapi (Myanmar), belacan (Malaysia), prahok (Cambodia), and bagoong (Philippines); and fermented fish sauce such as budu (Malaysia), patis (Philippines), and nuoc-mam (Vietnam). These products often require an acquired taste due to their strong aromas and distinct textures.

Fermented meat & fish products

Fermented meat & fish products, (A) fermented sausage, salami, ham, pepperoni, (B) fermented fish, (C) fermented fish paste, (D) fermented fish sauce

Meat and fish products made by microbial fermentation involve the manipulation of microorganisms to produce high-quality, safe, and sustainable food options. This innovative approach utilizes beneficial bacteria, yeasts, or fungi (staphylococci, lactobacilli, micrococci, yeasts, and molds) to transform raw materials into desired products through various fermentation processes. During fermentation, these microorganisms break down complex molecules found in meats or fish, resulting in the development of distinct flavours, textures, and nutritional profiles. Moreover, microbial fermentation offers several advantages compared to traditional meat and fish production methods. Microbial fermentation promotes the reduction of harmful pathogens such as salmonella or listeria while extending shelf life naturally through the presence of organic acid compounds. Furthermore, it allows for controlled adaptation to different dietary needs by producing low-fat or high-protein alternatives without compromising taste or texture. As a result, these microbial fermented meat and fish products provide an enticing option for consumers, seeking sustainable protein sources with enhanced nutritional benefits and diversified flavour.

22. ABE products

ABE production

acetone, butanol, and ethanol (ABE) production

Acetone, Butanol, and Ethanol are part of a group known as ‘ABE’ products, which are produced through the fermentation of sugars by certain bacteria (Clostridium, Saccharomyces, and Kluyveromyces). Historically used as solvents and fuels, they have found applications in various industries, including biofuels and pharmaceuticals.

23. Enzymes

Biofuel production

Role of enzymes in Biofuel production

Microbial fermentation is used to produce enzymes, which are essential catalysts in various industrial processes. Microorganisms used in enzyme production include Aspergillus, Trichoderma, Bacillus, Saccharomyces, Endothia, and Kluyveromyces. Enzymes such as amylases, proteases, and lipases are employed in the food industry, detergents, textiles, and even biofuel production.

24. Amino acids

Amino acid fermentation

Amino acid (L-Lysine) fermentation

Microorganisms like bacteria and yeast (Corynebacterium and yeast) are utilized to produce amino acids like glutamate, lysine, and tryptophan through fermentation processes.

25. Vitamins


Microbial fermentation is used to synthesize vitamins like vitamin B12, riboflavin (vitamin B2), and ascorbic acid (vitamin C). These vitamins have crucial roles in human health and are incorporated into various products, including dietary supplements and fortified foods. The most commonly used microorganisms in the production of vitamins include Eremothecium, Pseudomonas, and Propionibacterium.

26. Biopolymers

Biodegradable plastic


Certain bacterial species such as Pseudomonas, Bacillus, Rhodococcus, Staphylococcus, and Micrococcus can produce biopolymers like polyhydroxyalkanoates (PHAs) and polyhydroxybutyrate (PHB), which are biodegradable plastics. These biopolymers have applications in packaging, medical devices, and environmentally friendly alternatives to conventional plastics.

27. Pharmaceutical products

Vaccine production

Vaccine production

Microbial fermentation plays a pivotal role in producing complex molecules like antibiotics, vaccines, and other therapeutic agents for the pharmaceutical industry. Microbes such as E. coli, Penicillium, and yeast are genetically modified to produce human insulin, antibiotics (Penicillin), and growth hormones at large scales. As the demand for sustainable manufacturing continues to rise globally, industrial chemicals and pharmaceutical products made by microbial fermentation present an innovative solution that meets market needs and prioritizes environmental considerations.

28. Organic Waste Conversion

Microbial fermentation is used to convert organic waste, such as food scraps, agricultural residues, and sewage sludge, into useful products with the help of microbes including bacteria, actinomycetes, mold, and yeast. Beneficial microorganisms metabolize the organic matter, reducing its volume and generating byproducts like compost, biogas, and nutrient-rich effluents.

Use of microbes in waste management

Role of microorganisms in biofuel production and waste management

Microbial fermentation is a crucial process with immense potential in waste management. By harnessing the power of microorganisms, waste materials can be efficiently converted into valuable products such as biofuels, organic fertilizers, and bioplastics.

29. Biogas Production


Anaerobic fermentation, carried out by bacteria (Methanobacterium) in the absence of oxygen, is used to produce biogas from organic waste. Biogas primarily consists of methane and carbon dioxide, and it can be harnessed as a renewable energy source for electricity generation and heating.

30. Compost Production


Microbial fermentation is employed in the composting process, where microorganisms (actinomycetes, bacteria, and fungi) break down organic materials to create nutrient-rich compost. Compost is a valuable soil amendment that improves soil structure, water retention, and nutrient content, thereby enhancing agricultural productivity.

31. Wastewater Treatment

Biological waste water treatment

Microbial fermentation is integral to biological wastewater treatment systems, where microorganisms (Acinetobacter, Flavobacterium, Micrococcus, Nitrobacter, Nitrosomonas, Pseudomonas, etc.) help break down organic pollutants in sewage and industrial wastewater. This process reduces the organic load in water bodies and mitigates water pollution.

32. Biochemicals


Microbial fermentation can also be used to convert waste streams into bio-based chemicals, bioplastics, and other valuable products. Various bacterial species (Bacillus, Cupriavidus nectar, Azotobacter, Pseudomonas, methylotrophs, and Alcaligenes) and algal strains (Synechococcus, Spirulina, and Nostoc) are used for the same purpose. This approach contributes to the development of a circular economy by minimizing waste and reusing resources.

33. Reducing Landfill Waste

Landfill waste

By diverting organic waste from landfills, microbial fermentation helps reduce methane emissions, a potent greenhouse gas produced during decomposing organic matter in landfills.

34. Microbial Fermentation in the Gut

The gut is a prominent site of microbial fermentation, driven by the diverse community of microorganisms residing in the gastrointestinal tract. These microbes, collectively known as the gut microbiota, contribute to digestion, nutrient absorption, and various physiological processes. Gut microbiota includes E.coli, Bacteroidetes, Enterococcus, Enterobacter, Firmicutes, Actinobacteria, Klebsiella, Proteobacteria, Staphylococcus, and Fusobacteria. One example is the fermentation of dietary fibre and complex carbohydrates that the human body cannot digest on its own. Beneficial gut bacteria break down these substances, producing short-chain fatty acids (SCFAs) as byproducts. SCFAs are absorbed and play roles in energy production, gut health, and immune regulation.

Use of microbes present in human gut

Role of the gut microbiota in health and disease treatment

Microbial fermentation within the body has far-reaching effects on health, impacting digestion, immunity, and nutrient absorption. Beneficial microbes (E.coli, Lactobacillus, Proteobacteria, Clostridium, Streptococcus, Staphylococcus, etc.) present in the gut can compete with harmful pathogens for resources, limiting their growth and colonization. This phenomenon, known as colonization resistance, is an important defence mechanism against infections.

Microbial fermentation in the gut influences the development and regulation of the immune system. The gut microbiota helps educate and balance immune responses, preventing inappropriate reactions and enhancing defence against pathogens.

The gut microbiota contributes to the production of certain vitamins (such as B vitamins and vitamin K) and metabolites that impact health. For example, microbial fermentation of certain fibres produces butyrate, an SCFA that supports gut barrier function and has anti-inflammatory effects. Imbalances in the gut microbiota, known as dysbiosis, can lead to disrupted microbial fermentation processes and contribute to digestive disorders, such as irritable bowel syndrome (IBS). Restoring microbial balance through dietary changes and probiotics can help alleviate symptoms.

35. Fermentation in the Oral Cavity

Oral microbiome

Oral microbiome

Microbial fermentation also occurs in the oral cavity, where bacteria (Streptococcus, Actinomyces, Treponema, Staphylococcus, Lactobacillus, Selenomonas, etc.) metabolize sugars and produce acids. This process can contribute to dental health issues, such as tooth decay, if not properly managed through oral hygiene practices.

36. Microbial Fermentation in Muscles

Lactic acid production in muscles

Lactic acid fermentation in muscles due to strenuous exercise

Muscles can also experience microbial fermentation, particularly during strenuous exercise when oxygen supply becomes limited. This anaerobic environment prompts muscle cells to undergo fermentation to produce energy in the form of lactic acid. While lactic acid can cause temporary muscle fatigue and soreness, it is essential to the body’s energy production during intense physical activities.

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