Bakers Journal

Technical Talk: December 2010

November 11, 2010
By Dr. John Michaelides

Microbes are the bread and butter of the baking industry, producing the tastes, textures and appearances that customers expect, but some can hurt your business

For better or worse, microbes are a big part of baking.


Microbes are the bread and butter of the baking industry, producing the tastes, textures and appearances that customers expect, but some can hurt your business

Many microbes are involved in baking. Some are essential and beneficial for the process. Others contribute to consumer health. However, some microbes can be detrimental to product quality or even dangerous.


The main micro-organism we are all familiar with is yeast. Yeast is essential in the fermentation process for yeast-raised baked goods. It produces the carbon dioxide that assists in the leavening of the bread. Yeast also contributes to the flavour of baked goods. Different strains of yeast are available; which strain you need depends on your production process and your final product. For example, products destined for freezing require yeast strains containing higher amounts of the chemical trehalose to survive freezing and remain relatively active during thawing and baking. Acid-resistant yeast strains are available that will function normally in sourdoughs with very low pH, where normal yeast strains would not be active. More recently, yeast has been modified to naturally increase its vitamin D content. Yeasts and moulds naturally contain ergosterol, which converts to vitamin D when exposed to UV light. High vitamin D yeast is now commercially available. This is good news, because recent research has identified vitamin D as a very important agent for human health.

Other microbes essential for the baking process are sourdough cultures. Sourdough production involves a long fermentation process that allows the natural bacteria to grow and ferment, producing the characteristic flavours. These bacteria are mainly varieties of Lactobacilli and can be divided into two groups: the homofermentative, which produce only lactic acid, and the heterofermentative, which also produce acetic acid, alcohols and carbon dioxide. These cultures provide the flavours as well as some leavening action. The bacteria involved in the sourdough process vary with the different grains. Recent research has identified those involved in sourdough production from gluten-free grains, providing the opportunity to develop products for people with celiac disease.

Indirectly, bacteria and fungi are used for the production of ingredients such as amylases and other enzymes that play a fundamental role in the baking process.

Incorporating friendly bacteria or probiotics into food has generated great interest recently. Probiotics are collectively known as all the beneficial bacteria in the colon of the human body. These friendly bacteria ferment the prebiotic substances (food for probiotics) in the large intestine, decreasing the colon pH. This assists in reducing pathogenic bacteria and viruses. Probiotics contri-bute to numerous health benefits, including prevention of chronic diseases, improving the immune system and increasing the absorption rate of minerals and vitamins into the body. Some common probiotics include species of the genus Lactobacillus, and Bifidobacterium. We can increase the numbers of these micro-organisms in our colon by eating more prebiotics, taking high doses of probiotics orally or consuming probiotics in our food.

The main obstacle to applying probiotics to baked goods is that the baking temperatures required kill the majority of these beneficial bacteria. However, new technologies can provide tools to partially overcome this problem. Probiotic cultures are now available in microencapsulated form designed to provide a viable solution to this problem. In addition, some of these bacteria form spores when they are exposed to high temperatures. The spores can survive high temperatures for long periods of time, so delivering these bacteria in spore form is another solution.

In addition to the beneficial microbes, there are many that contribute to spoilage, reducing the quality of baked goods. Yeasts and moulds are characteristically a problem that decreases the shelf-life quality of these products. Although they are normally killed by the baking temperature, they are often present in the environment and cross-contaminate the freshly baked goods. Similarly, bacteria can contribute to spoilage. However, unlike yeast and moulds, not all bacteria are killed in the baking process.

Rope bread is a classic problem associated with these types of surviving bacteria. The rope is caused by the bacterium Bacillus mesentericus, a spore former. Although the normal baking temperature will kill all the growing and vegetative bacteria, it will not eliminate the spores. After baking and during cooling, the rope spores will germinate and produce the characteristic ropy structure of the interior of the bread. This structure is the result of the action of proteolytic and amylolytic enzymes secreted degrading the proteins and starches. The bread will also have a characteristic ripe melon odour. Although using preservatives in bread formulations diminishes the incidence of rope in modern products, the return to natural breads may result in a resurgence of this problem. Other spoilage bacteria include Serratia marcescens, which forms red spots on breads and results in what bakers call bleeding bread.

Some micro-organisms can cause serious problems. Pathogenic bacteria may be introduced to baked goods by cross-contamination from the environment, human handling or other ingredients such as fillings and creams. These can either cause infections such as Salmonella, E. coli and Streptococcus, or produce toxins such as Staphylococcus aureus, when they proliferate in the baked goods and cause poisoning.

One potential problem bacteria is Bacillus cereus. It is frequently present in uncooked rice, and its heat-resistant spores can survive cooking. If cooked rice is held at room temperature, the spore will germinate, grow and produce a heat-stable toxin that can survive reheating. Although mainly present in rice, it has been reported in other grains, so it is important to consider these bacteria when manufacturing multigrain breads.

Other dangerous implications with micro-organisms in baked goods can be indirectly linked to moulds and the production of mycotoxins. Several fungi have been associated with grains that result in the production of mycotoxins that may cause severe or long-term complications to humans. Ergotism, a particularly dangerous kind of food poisoning, has been long associated with the fungus Claviceps purpurea that infects rye grains. The resulting fungal mass contains many chemicals that can cause serious health problems. In order to control the incidents of ergotism, governments introduced strict limits on the number of infected grains in wheat and other cereals.

Another mycotoxin-producing fungus associated with wheat is Fusarium graminearum, which among other toxins produces vomitoxin. The levels of vomitoxin in wheat and flour are also regulated. 

While microbes are an essential part of the baking process, it is important to understand the good, the bad and ugly.

Dr. John Michaelides is Guelph Food Technology Centre’s director of research and technology. For more information, or fee-for-service help with product or process development needs, please contact the GFTC at 519-821-1246

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