Advanced Food Microbiology

Module 9: Course assessment

Microbiology and food spoilage


Microbial spoilage of foods is a massive problem globally. It has been estimated that about 25% of all foods produced globally are lost due to microbial spoilage.

Food spoilage results when microbiological, chemical, or physical changes occur, rendering the food unacceptable to the consumer. Microbiological food spoilage is caused by the growth of microorganisms which produce enzymes that lead to objectionable by-products in the food.

Microbial growth can also produce visible discolouration or (in the case of mould spoilage) outgrowths from the food product.

Spoiled food is not necessarily harmful, although it is considered unpalatable and therefore rejected by the consumer.

The numerous sources of microbial spoilage come from undesired yet ubiquitous micro-organisms which can originate from the natural habitat, e.g. soil, water, air, spoiled raw materials, biofilms on the surface of equipment, personal hygiene of food workers.

Most foods serve as a good growth medium for many different microorganisms. Considering the variety of foods and the methods used for processing, it is apparent that practically all kinds of microorganisms are potential contaminants and can cause changes in appearance, flavour, odour and other qualities of foods.

These degradation processes include putrefaction (proteolytic microorganisms), undesired fermentation (saccharolytic microorganisms) and rancidity (lipolytic microorganisms).

Bacterial spoilage

Food spoilage can occur for a variety of reasons, including contamination by microorganisms such as lactic acid bacteria and Pseudomonads. Lactic acid bacteria (LAB) are known as facultative anaerobic bacteria, in other words, they tolerate oxygen but thrive without air.

This group of bacteria often play a positive role in the food industry and account for some of the special tastes consumers enjoy – for fermenting pickles or sauerkraut, for example – but they can also cause major spoilage, hurting customers’ perception of a brand or product.

Consumers expect food to have a long shelf life and enjoy the convenience of products that can keep for an extended period of time. From a commercial point of view, this is also important given the fact that considerable time can elapse in light of transportation logistics and storage before a product is consumed.

Foods that have high acidity/low pH or are vacuum-packed − like salad dressings, tomato-based products and processed meats − are particularly susceptible to spoilage from LAB. These need to be carefully monitored to avoid contamination.

Undesirable spoilage caused by LAB include:

  • Greening of meat;
  • Gas formation in cheese;
  • Bloating or exploding of vacuum sealed pouches;
  • Off flavours – cheesy, malty, acidic, foul, sour;
  • Slime on meats
  • Ropy beverages or dairy

LAB are considered indicators since conditions favourable to their growth also favour Clostridium botulinum which is a very dangerous bacteria for humans. Therefore, testing, monitoring and controlling lactic acid bacteria in food production is part of a strong food safety program that helps prevent other contaminants as well.

The economic burden on the food industry due to Pseudomonas spp. spoilage has been calculated as approximately one-third of the edible parts of food produced globally.

The dairy sector alone accounts for about 25–30% of these losses; in industrialised countries, half of these losses are directly related to the consumption stage.

Around 70% of cold tolerant spoilage organisms have been found to be Pseudomonas species, representing a large section of food losses.

They are easily spread in production environments, being both readily transferrable via clothing and resistant to many sanitisers that the food industry relies upon.

Yeast spoilage

Colony morphology – Zygosaccharomyces species

Certain yeast species are known to cause significant spoilage in a range of food and beverage products – most notably Zygosaccharomyces bailii, Z. bisporus and Z. lentus in low pH products such as mayonnaise, salad dressings and particularly fruit juices.

Yeasts can enter the food production area as secondary contaminants on the clothing and bodies of workers, or as part of the natural microbial flora on raw ingredients (particularly fruits). Once established they are very difficult to remove from the production environment due to their resistance to many sanitisers.

Yeasts become the dominant contaminants of food and beverage products when competition from other microorganisms (for example, bacteria and mould) is restricted by low pH, the presence of preservatives (especially benzoic and sorbic acids) and high sugar and/or alcohol concentrations.

In the definitive work by CSIRO scientists John Pitt and Ailsa Hocking (“Fungi and Food Spoilage”), 12 key yeast species were identified as being of significance in food processing/production facilities. They found that most spoilage by yeasts is opportunistic and dependent on breakdowns in the hygiene process or GMP of the facility.

These 12 species, however, have specific resistance capabilities that allow them to cause a range of issues in food production areas, from inherent resistance to preservatives, to being osmotolerant (ie requiring less water, therefore able to grow in high sugar solutions). Of these 12, the one that we have seen causing most issues in recent years has been Zygosaccharomyces bailii​

11 Zygosaccharomyces species together with foods they have spoiled

Foods particularly at risk of spoilage by these yeasts tend to be acidic (pH 2.5-5.0) and contain high concentrations of fermentable sugars. These products include soft drinks, sugar syrups, jams and preserves, honey, tomato sauce, mayonnaise and wines.

Typical spoilage properties include the generation of taints, odours and off-flavours, hazes and excessive gas production, which can subsequently cause the distortion or explosion of packaging.

Zygosaccharomyces bailii is one of the most significant and important spoilage organisms in modern food and beverage production. Not only does it tolerate conditions that normally destroy or inhibit microbial growth, but it positively flourishes in these conditions.

It tolerates a wide range of stressful conditions – for example, it is resistant to numerous preservatives (such as acetic, lactic, propionic, benzoic, sorbic acids and sulphur dioxide). It can tolerate high ethanol conditions (>15%), which causes major losses in the wine industry. It vigorously ferments glucose and fructose, making it also of particular significance in the premium cold pressed juice industry.

It can do all of this in the absence of oxygen, as long as there is a sufficient source of sugary food. Finally, just one viable cell is enough to spoil over 10 litres of beverage, so even detecting extremely low numbers of this organism in a batch is not sufficient to ensure that the product is not spoiled. ​

With all of this bad news, how do you protect your products from this organism? One way is to ensure that sucrose is the only carbon source in the product – Z. bailii cannot readily grow in products where sucrose is the only carbon source, as it requires time to convert the sucrose into glucose and fructose. The lag time is therefore increased to 2-4 weeks (instead of a matter of hours) and product deterioration will only be noticeable 2-3 months after manufacture. Therefore, using sucrose to sweeten synthetic soft drinks offers some control over spoilage by Z. bailii.​

Mould spoilage

One of the key differences between yeast and mould spoilage of foods is the ability of moulds to form toxins which inhabit the food and can cause a range of illnesses and potentially death.

As with yeasts, mould growth is supported in a wide range of food products, as they are tolerant to low pH and water activity and can derive nutrition from multiple sources, including carbohydrates, organic acids, proteins and lipids. This is why you see moulds on fruits and fruits juices as well as on breads and baked products.

Although there are many hundreds of different mould species that have been isolated from foods, significant spoilage has been found to be limited (as with yeasts) to a relatively small group – around 10. In many instances, only around 1-3 species are responsible for spoilage, but it hasn’t been until the advent of more sophisticated analysis techniques that this has been established.

Mycotoxins are a serious health risk associated with moulds – over 400 types of mycotoxin have been identified, although around 12 key compounds are found to be common in human foods.

The moulds that produce these mycotoxins grow on a variety of different foods, including: cereals, nuts, spices, dried fruits, apples and coffee beans. Because the toxins are chemically stable, they are able to survive processing and therefore present a potentially serious hidden threat to human health.

Common types of mycotoxin include: aflatoxin, ochratoxin A, patulin and fumonisins. The range of illnesses include acute poisoning which can manifest soon after consuming food containing the toxin, to long term affects such as cancer and immune deficiency.

The World Health Organisation has established (through the Codex Alimentarius Commission) maximum levels for mycotoxins in foods. The levels are set very low due to the extreme toxicity of these compounds – for example, the limit for patulin in apple juice is 50 micrograms per litre (a microgram is one millionth of a gram, or one billionth of a kilogram).

For food producers, one of the key controls in minimising the risk of incorporating mycotoxin containing ingredients in the final product is through an approved supplier program as part of the HACCP plan. Raw materials suppliers will need to demonstrate through laboratory analysis certificates that their products have been tested for mycotoxins and that they are not present at levels in excess of those contained in relevant regulations.

For example, in the food standards code, Schedule 19, section 5 there is a maximum level of 0.015mg/kg of aflatoxin permitted in peanuts and tree nuts.