Common undesirable microorganisms in the food industry and how to prevent them

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Microorganisms, or microbes, play an important role in breaking down natural matter in the environment. Without them, there would be a build-up of waste, and this wouldn’t be recycled back into the food chain. Because of their key job in continuing the natural recycling of nutrients, they are found basically everywhere in the environment: in the soil, water, air, inside living creatures and on most surfaces that we come into contact with on an everyday basis.
As a result, microorganisms are the reason food spoils if left alone for a certain amount of time.


Every year, thousands of tons of food are tossed out as waste due to spoilage or contamination. Spoilage causes food to change in a way that makes it less desirable, such as the colour, texture or taste changing. Contamination can sometimes occur without any noticeable change in the food itself. Eating food with high amounts of harmful microorganisms can cause a person to become sick or unwell, and this is why it is so important to take the steps to lessen or prevent them from growing. With regards to the food industry, are two specific classes of microorganisms which they look out for: those which affect the quality of food by causing spoilage, and those affect the safety of food, or the health and safety of consumers.

Microorganisms which impact consumer safety

If you’ve ever had food poisoning, or felt ill after eating something, then you’ll understand why these microbes are so important to food producers.
Many of these microorganisms are ones that naturally grow and develop within the stomachs or bodies of living animals, and contaminate food through contact with faeces, polluted water, or other surfaces where the microbes have been growing. Others are present on your skin or naturally in the environment. While many of these are harmless, certain strains can cause gastrointestinal illnesses when eaten. These usually grow best at around the same temperature as our bodies (25 – 39⁰C), but can survive within a wide range at lower and higher temperatures as well: between 5⁰C and 60⁰C. There are many microbes which can cause a person to become sick, including bacteria, viruses, fungi and some forms of small parasites. How likely you are to encounter these microbes will depend on where they are found. Some microbes grow better on specific types of food or are more likely to contaminate the food if it comes from a specific environment.

The microbes either make you ill by directly attacking your body, or you can be poisoned or have a reaction to the presence of toxins produced by these microbes. Toxins are small chemicals produced by growing microbes which your immune system recognises as harmful and tries to destroy in order to protect you. They are difficult to get rid of because they aren’t destroyed under extreme conditions such as high temperatures. This is why even if you kill off microbes present on food, these is a chance that you could still become ill from the presence of toxins.  Some examples of microbes that cause illness are: Listeria monocytogenes, Tapeworms, E. coli, Salmonella spp., Shigella, Norovirus, Hepatitis A and Aspergillus spp.

Microorganisms which cause food spoilage

Microbes which cause spoilage are a big concern to food producers as they are widespread and often grow under a much wider range of conditions than illness-causing microbes. These microbes are usually types of bacteria or fungi such as yeasts or moulds and they consume or break down parts of food by releasing enzymes. The enzymes decompose part of the food, resulting in the release of simpler nutrients and this results in spoilage.

It is a good idea to never consume spoiled food, as it is possible to become ill from toxins produced during spoilage, such as mycotoxins from types of moulds. Living plants and animals can prevent microbes from causing spoilage. This is usually done through a protective layer as well as a type of defensive internal system which kills off microbes that do manage to access the body. For example, many fruits have a waxy layer that protect them from the outside environment. When this is cut or bruised, microbes will have access to the vulnerable flesh beneath the surface. Citrus fruits usually combat this with a high acidity, creating an environment that bacteria cannot live in. Some examples of microbes which cause food spoilage are: Lactobacillus, Carnobacteria, and Clostridium spp.; Candida and Saccharomyces yeasts; and Aspergillus spp.

Factors which affect the growth of microorganisms

Several factors will determine which microbes can grow in certain environments. These can be summed up with the acronym: FATTOM

F – Food. Are there nutrients available for the microbe to consume?
A – Acidity. What is the pH of the environment, and can the type of microbe survive it?
T – Temperature. What is the temperature of the environment?
T – Time. Does the microbe have enough time to grow and multiply unimpeded?
O – Oxygen. Some microbes need access to oxygen to grow.
M – Moisture. Most microbes grow best in wet environments.

Depending on the amount and range of these factors, different microbes will find it easier to cause spoilage on different types of food. For example, yeasts and moulds are usually able to grow at much lower pH levels than most bacteria and are more likely to grow on fruits and some vegetables. Clostridium botulinum, the bacteria best known for the deadly toxin that causes botulism, grows well without the presence of oxygen, which is why it is of great concern in canned foods. As mentioned previously, some microbes grow better at different temperatures, with many illness-causing ones favouring temperatures close to the human body. Listeria monocytogenes can grow at very low temperatures as well, even around the range of 1-5⁰C, making it able to grow on foods kept within refrigerators if given enough time.

High risk and low risk foods

Some foods are more likely to be contaminated with microbes than others based on their compositions. In the food industry, these are usually termed high risk foods and low risk foods. Low risk foods are those which are less likely to become contaminated or undergo spoilage, such as dried products, unprocessed fruits and vegetables, uncooked grains and highly salted or pickled foods. These foods can be stored for longer periods of time without spoilage occurring if kept in good condition. Pickling and salting are a common means of raising the acidity and lowering accessible water levels in foods, making it harder for microbes to grow on them. High risk foods are the opposite and are expected to undergo spoilage or become contaminated very quickly if not stored correctly. These include cooked and ready-to-eat foods, meat, milk products and unshelled eggs. The high protein content, low acidity and water content of these products make them a good target for most microbial species and spoilage will often occur within a few days once exposed to microbe rich environments.

Preventing food contamination and spoilage

There are several ways to store and protect food products that both the food industry as a whole and consumers can practice to prevent or lessen spoilage and contamination by microbes.

1. General good hygiene practices

Washing your hands regularly and keeping your food storage and preparation areas clean are some of the most effective means of preventing microbial species from accessing your food. The food industry has a legal obligation to adhere to laws regarding good hygienic practices for food handling businesses (such as R638 of the FCD Act) and must implement policies and procedures to ensure that their premises adhere to these regulations.

2. Storage conditions

Make sure to read the labels on your foods so that you know how to store them correctly. Some products can be stored in dry areas while others need to be refrigerated or frozen. Freezing and refrigerating food is a good way to hinder the growth of microbes but does not outright kill them. If given enough time, some species of microbes will grow and multiply on the food, making it unsafe to eat. Cooked and ready-to-eat meals should be stored at a high enough temperature to kill off and prevent the growth of microbes. In South African regulations, this is usually defined as 60⁰C. There are general guidelines provided in R638 on what foods need to be stored at different temperatures.  For instance, while frozen vegetables can be stored at least -12⁰C, frozen fish and ice cream must be kept at least -18⁰C (Annexure E). Notable ranges are:

  • The Danger Zone between 12⁰C and 59⁰C, the wide range in which most microbes can grow.
  • The Extreme Danger Zone between 25⁰C and 39⁰C where most pathogenic microbes grow the best.

If a food product falls out of the range at which it is supposed to be stored, there are additional guidelines for what is acceptable to return to the correct conditions and when to dispose of the food. For example, cooked food can only be left up to 4 hours before being eaten, and they can only be warmed up again once. Otherwise, the food must be thrown away. Toxins could have built up over that time and the food may make you ill if consumed.

3. Keep high and low risk foods separate

Low risk foods are more likely to be stored in conditions where they can be exposed to microbes without fear of undergoing rapid spoilage, and therefore should remain completely separate from food that can spoil rapidly. Cross-contamination can occur if the foods are stored close together or prepared using the same utensils, such as chopping boards and knives used to cut raw meat used again on cooked meat.

4. Cook food properly

Food should be cooked at temperatures over 60⁰C, with the centre of the product reaching at minimum 70⁰C for at least 15 seconds to kill harmful microbes.

5. Consume or use food within the recommended timeframe

Best before dates on food labels indicate the expected time by which a product should be used. For certain foods, the label will also specify how long you can keep the food once opened. While there are instances that a product might still be good after its expiry date, it is always good practice to ensure that you try to use them within the expected timeframe if you want to avoid possible illnesses.

6. Always inspect your food carefully before consuming

Use your intuition and your senses. Don’t buy or eat a food product which you feel could be contaminated. If the food smells, looks or feels wrong without a good explanation, avoid it. Never use a can which is bloated or dented as it might contain harmful microbes. If you handle food which you know might be spoiled or contaminated, don’t touch unspoiled food before washing your hands as this will transfer the microbes.


Microorganisms aren’t going anywhere any time soon, and the best approach we can take to handling them is to understand and adhere to good practices in order to prevent them from negatively impacting our lives. By understanding the role that microbes play in breaking down food and how food can become contaminated with microbial species, we can better identify those which can be harmful to us or cause food to spoil if not treated accordingly. Different species of microbes will be of greater concern to specific types of food depending on their compositions and how they are processed or stored. Factors which will affect this are identified by the acronym FATTOM (see above).

Keep an eye out for later articles as we explore the different types of microorganisms of interest to sections of the food industry.

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