Microorganisms Found in Food

Food is a basic human need for the growth and development of our body. It is a source of nutritional components, antioxidants, and essential oils, which benefit our health and promote the function of our body. 

Microorganisms found in Food
Microorganisms found in Food

Various factors like microorganisms, enzymatic reactions, and storage participate in food preservation and accelerate food spoilage. Food microorganisms are categorized into two forms: one that is used for food preservation and one that promotes food spoilage. 

The involvement of microorganisms in food preservation techniques increases food’s shelf-life and prevents the degradation of nutritional components of food. At the same time, the presence of microorganisms in rapid number accelerate the growth of microorganisms in food.

Use and Effects of Microorganisms in Food

Every food gets spoiled after a specific time of harvesting or slaughtering. Food spoilage is undesirable changes in texture, smell, taste, or appearance cause foods to be rejected for consumption. Microorganism is the leading cause of spoilage of foods. However, microorganisms are also helpful in changing food’s color, flavor, and texture during growth or processing. The activity of microorganisms in food are:

  1. Production: Production and preparation of food is the process of transforming raw ingredients into edible products. Aspergillus niger is a mold used in the industry for manufacturing citric acid and enzymes. Saccharomyces cerevisiae is the yeast used for the production of bakery items. Clostridium butyclicum is a bacteria used for making sour milk and cheese. 
  1. Preservation: Food preservation is followed after harvesting or slaughtering to elongate the shelf-life of food and prevent microbial growth. Fermentation is the metabolic process for conservation, where the production of alcohol and gases takes place. Saccharomyces cerevisiae is the yeast that takes part in the fermentation of wine, beer, and other alcoholic beverages. Lactic acid bacteria take part in the fermentation of yogurt, pickle, and kimchi. 
  1. Spoilage: Microorganisms not only promote production and preservation but also accelerate spoilage. Pseudomonas is a bacteria that plates an essential role in the spoilage of milk and meat. Saccharomyces cerevisiae is the yeast that participates in the fermentative spoilage of high-sugar foods and beverages. Aspergillus flavus is the mold that produces mycotoxins in food. 

Types of Food Microorganisms

Food is highly affected by significant microorganisms, bacteria, fungi (yeast and mold), viruses, and parasites.

The action of some microbial enzymes in the food plays a vital role in prevention and spoilage. These microorganisms are ubiquitous on the surface of nearly all fresh food products. For preparing processed foods, microorganisms are added because the enzymatic action of microorganisms is required.

This post further discusses how the different types of microorganisms play a role in promoting the shelf-life of food and boosting spoilage.


Bacteria are the most common and significant microorganisms, participating in the preservation and spoilage of food. Lactic acid bacteria (LAB) can produce organic acids like hydrogen peroxide, inhibiting the growth of harmful bacteria. LAB can also inhibit the growth of pathogens and enhance the development of immune cells and antibodies. Yogurt, kimchi, miso, and pickles are high in probiotic strain. 

Spore-forming bacteria are usually seen in heat-treated foods, as such bacteria can survive even in high temperatures. They spoil not only food but also produce neurotoxins causing harm to humans. So these are also called pathogens. They can contaminate hermetically sealed low-acidic foods like fish, puddings, cauliflower, artichoke, and high-acidic foods. Psychrotrophic spore-formers have been recognized to cause spoilage of refrigerated foods. 

Beneficial and harmful bacteria

Beneficial: Lactic acid bacteria are considered beneficial because they help boost immunity and enhance lactose digestion. 

  1. Lactobacillus can ferment sugar and prevent the growth of spoilage microorganisms. It helps to prevent diarrhea in small children and adults.
  2. Leuconostoc is used in the industry for the fermentation and production of cheese and cultured milk. It lowers the pH and promotes the growth of good bacteria in the body.
  3. Streptococcus is used for the production of fermented dairy products. It possesses anti-inflammatory action and boosts immunity.

 Bacillus sporothermodurans, Bacillus amyloliquefaciens, Lactococcus spp. and Clostridium botulinum are also healthy bacteria.

Harmful: The activity of both spore-forming and non-spore-forming bacteria causes food spoilage and disturbs our health by causing gas gangrene and neurotoxicity. 

  1. Clostridium botulinum is a toxin-producing bacteria. It produces gas which can lead to respiratory and muscular paralysis. 
  2. Brochothrix thermosphacta is a spore-forming bacteria that produce volatile organic compounds that can damage the central nervous system.  

Bacterial spoilage can be prevented by reducing the water activity in the food.


Yeasts are unicellular microbes resembling fungi, larger than bacteria. It reproduces by budding and is classified as Ascomycetes and Basidiomycetes. Yeast has been used for the fermentation of alcoholic beverages and the leavening of bread. Yeast produces lytic enzymes (lipases, proteases, and cellulases) and gas, which can lead to the consumption of organic acid. Reduction of organic acid in food can result in off-flavor and food discoloration. Yeast is also used in starter culture to produce cheese, vinegar, and fermented vegetables. Generally, food with high acid, low pH, high sugar, and high salt is prone to yeast spoilage.


  1. Saccharomyces cerevisiae is used for the fermentation of alcoholic beverages and the production of biofuel in the industry. It is used as a probiotic in humans and animals.
  2. Candida humilis is used in bakeries as a leavening agent. It benefits humans by reducing inflammation and promoting good bacteria in the gut. 

 Debaryomyces hansenii and Schizosaccharomyces pombe are also considered healthy yeast.


Yeast is generally considered safe for consumption. However, excessive consumption of yeast can cause allergic reactions and gastrointestinal issues. Consumption of alcoholic beverages high in Schizosaccharomyces pombe degrades our health. 

Yeast spoilage is prevented by using chemical preservatives like sodium benzoate, which deactivate the yeast and hinders its multiplication. 


Molds are fungi that can grow within a wide range of water activity (aw), pH values, and temperature making them highly adaptable to different environments. They are multicellular in structures, visible to the naked eye, and generally grow from spores present in the air. Edible mold is essential in the cheese industry, used to produce “blue cheese.” 

However, not all types of molds are safe for consumption. Molds, when present in food, utilize carbohydrates, organic acids, protein, and lipids, resulting in their growth on acidic products (fruits and juices) and foods with medial moisture content (bakery products) where other microorganisms like bacteria can not grow.


  1. Penicillium roqueforti is used in the industry for the production of blue cheese. It is beneficial for balancing cholesterol levels and maintaining blood pressure.
  2. Penicillium camemberti is also used in manufacturing cheese like Camembert and Brie cheese. They are a good source of protein, calcium, and other nutrients.
  3. Rhizopus oligosporus is used as a starter culture in the production of tempeh. It is used for fermenting vegetables. It possesses anti-inflammatory reactions and improves digestion.


  1. Mucor is associated with decaying organic matter and food products. Excessive consumption of mucor weakens our immune system and affects the brain and lungs.
  2. Botrytis is used to produce certain beverages and cheese, but it produces mycotoxins and compromises the immune system. 
  3. Alternaria is unsafe for human health because it causes an allergic reaction, produces mycotoxins, and causes respiratory issues.  

Mold growth can be prevented by lowering the moisture of food and the humidity level of the room where the food is stored. 


These are acellular organisms that replicate only inside the living cells of an organism. Viruses are usually known as microorganisms that degrade health. Viruses do not cause food spoilage in the same way as bacteria and fungi, as viruses require a living host to multiply and can not grow or reproduce on their own. One suffers from foodborne illness if the foods spoiled by viruses are consumed.


  1. Bacteriophage is a virus that destroys bacteria and also possesses antibiotic effects. 
  2. Oncolytic viruses are known for destroying specific cancer cells.


  1. Rotavirus is a contagious virus that degrades salads and shellfish. It causes diarrhea, vomiting, and fever in humans. It can also cause dehydration. 
  2. Norovirus plays a significant role in spoiling fresh fruit and leafy vegetables. It causes gastrointestinal illness and dehydration. 
  3. The consumption of contaminated food and water can transfer hepatitis A. This virus directly affects the liver.

Cleaning food before consumption, handwashing, and proper cooking can prevent food spoilage from viruses and protect us from foodborne illnesses. 


Parasites are unicellular or multicellular organisms that survive on the host for growth and multiplication. Parasites include various protozoa and worms. Human parasites are broadly classified into two groups: Endoparasites, which cause infection and include protozoa, and ectoparasites, which live on the skin’s surface and feed on blood and body fluid. These parasites enter the human body through unpasteurized milk, uncooked and undercooked meat, fish, and contaminated water. 


  1. Helminths are considered adequate for treating autoimmune diseases, such as Crohn’s disease (inflammatory bowel disease) and multiple sclerosis (a condition that affects the brain and spinal cord). The parasites are believed to reduce inflammation and provide relief from such symptoms.


  1. Nematodes infection includes hookworm infection, which can cause anemia and malnutrition. It spoils foods like carrots and potatoes. 
  2. Cestodes, also known as tapeworms, infect the intestines of humans and other animals. Cestodes transfer from raw or undercooked meat (beef and pork) into our bodies.

Proper handling and cooking practices can prevent the spoilage of food from parasites. 

Factors Promoting Microbial Effects on Food

Various sectors promote spoilage of food through microbial effects. An imbalance in climatic conditions and enzymatic reaction exposes the food to spoilage and degrades its physical and nutritional characteristics. Some significant factors affecting microbial behavior in food are temperature, water activity, and pH.  


Temperature is the most critical factor affecting microbial growth or behavior in food. 

Microorganisms are classified into three groups concerning their growth temperature domain: Psychrotopes (grow well below 7℃ with an optimal rising temperature of 20-30°C), Mesophiles (grow well between 20-45℃ with an optimal increasing temperature of 30-40℃), and thermophiles (grows well higher than 45℃ with an optimal rising temperature of 55-65℃). 

Most food-borne pathogens are mesophilic pathogens.

Storage of food at lower temperatures effectively slows the metabolic activity of food and chemical reactions and prevents the growth of microorganisms. 

Lowering the temperature increases the lag time of food-borne microorganisms, which can extend the shelf life of minimally processed, pasteurized, and raw foods.

However, it is essential to know that low temperatures can inhibit the growth of mesophiles and thermophiles, but psychrotrophic microorganisms can still grow at refrigerating temperatures. It is necessary to adjust the extrinsic and intrinsic parameters to inhibit the growth of psychrotrophic organisms, which can prevent spoilage and increase the shelf life of food. 


pH refers to the acidity or basicity of any components, which ranges between 0 to 14, where pH less than 7 is acidic, and more than 7 is basic, 7 being neutral. 

All microorganisms have an optimal pH range of growth and survival and are more sensitive to internal pH change than external. A significant change in pH can modify the ionization of amino-acid functional groups and disrupt hydrogen bonding. This activity leads to a change in protein folding denaturation and loss of viability. 

The minimum and maximum pH values tolerated by each microbial species depend upon various factors like the type of acid used, metabolic enzymes, protein synthesis, or genetic materials. Most microorganisms grow at a pH value close to 7, but few can grow at a pH value below 4.

Pathogenic bacteria are more sensitive to pH than filamentous fungi and yeast. Lactic acid bacteria can grow below pH 2. 

Water activity (aw)

It measures free water available in food for biological and chemical reactions. Water activity is an essential factor affecting microorganisms’ growth and survival. Water activity beyond the optimal range reduces the vital metabolic functions of the cell and physiological processes like nutrient absorption. 

Bacteria need high water activity for growth and multiplication, comparing fungi. Most bacteria associated with food spoilage can grow at water activity above 0.91, whereas most filamentous fungi can grow at water activity low as 0.80.

Staphylococcus aureus can grow at a water activity of 0.86, and Clostridium botulinum needs a water activity of at least 0.94. Yeast can grow at lower water activity than bacteria.

Xerophilic molds can grow at a water activity of 0.65.


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Diksha Koirala

Diksha Koirala is a recent graduate student in Food Technology. She developed an interest in the relationship between microorganisms and the environment and their impact on the food and food industries. She is sharing her knowledge here to make the world understand microorganisms and the role it plays in our daily life.

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