Microbial contamination of food and beverage products is a potentially catastrophic occurrence resulting in foodborne illness or food spoilage. The same nutritive properties rendering cheese and dairy products also provide an ideal growth medium for microbes if contamination occurs. Although production and distribution of food is tightly regulated there is little secondary inspection of these products in the U.S., so outbreaks of foodborne illness are typically only detected after consumers become sick. An outbreak can lead to costly product recalls, regulatory fines, negative consumer sentiment, loss of brand value, idling production facilities and civil or potentially criminal legal proceedings. Microbial contamination also leads to product quality issues and spoilage, resulting in loss of product, decreased shelf life and unhappy customers.

Microbial contamination

Microbes are the most thriving life form on Earth, whether measured by total mass, number of species or number of cells. There are more bacterial cells in an individual human than there are cells. Microbes are found in almost every known environment and most pose no risk or are beneficial; many are necessary to prepare the foods and beverages we consume. As evidence of the importance of microbes, some of the world’s best microbiologists are in the brewing, baking and cheesemaking industries. Prevention of foodborne illness or food spoilage requires carefully balanced microbial control through removing harmful bacteria from production equipment and process ingredient streams, while not adversely affecting food quality or preventing the growth of desired microbes. A modern, well-run production facility will employ multiple techniques to prevent contamination in every step of their process. Table 1 contains a partial list of microbes of concern in cheese production.

Harmful microbes can generally be categorized into four groups: Bacteria, fungi, protists and viruses. Table 2 contains a partial list of pathogens potentially present in untreated domestic wastewater and the categories in which they fall. Bacteria and fungi are most worrisome in cheese production, as they are principally responsible for spoilage and foodborne illness. These organisms can use the chemical energy of affected food products to multiply and spread; one viable cell can become billions within a single day if growth conditions are ideal.

Both protists and viruses can be troublesome and highly dangerous pathogens in humans but are less likely to cause spoilage due to their life cycle. Viruses are only capable of reproducing when they hijack the cellular machinery of another living organism, while protists can only reproduce in aquatic environments or in a host. Neither viruses nor protists can directly use food energy for growth, and therefore they do not cause spoilage.

Microbes have remarkable mechanisms by which they can protect themselves and ensure their survival. Some bacteria are capable of forming a biofilm consisting of a slimy mass of extracellular material protecting the individual cells from damage by light, oxygen, disinfecting chemicals and other environmental harms. Microbes that colonize existing biofilms gain equivalent protection from efforts to inactivate them. Many bacteria and protists have the ability to enter a dormant cystic state when environmental conditions are unfavorable. Cysts are much more resistant to damage than the active state. They can survive extremes in temperature, large doses of radiation, including ultraviolet (UV) light, high salinity and severe dryness, as well as remain viable for incredible periods of time.

Routes of microbial contamination

Most cheese plants will contain at least some level of microbial contamination even with rigorous and appropriate control measures in place. Microbes can elude detection and inactivation. For example, even the tiny gap between the threads of a screw and the threads in the hole can harbor thousands of bacteria. Many artisanal cheeses gain their unique characteristics from the natural microbes present where they are produced, but large-scale production requires greater consistency than artisanal methods typically provide. A well-designed and rigorously applied hygiene plan is required to prevent the low-level natural microbial background from reaching levels that affect quality or safety.

In addition to the microbes already present, there are many paths through which microbes can enter a production facility. Cheese production requires water, milk and other ingredients, along with production equipment, production and packaging materials, personnel and ventilation. Each of these has the potential to introduce microbes into the production area. Microbe control procedures should identify the risk of contamination from every potential source and take steps to prevent it. As an example, the casing of a groundwater well that has corroded near the soil surface can admit untreated wastewater or farm runoff in the event of flooding or significant rainfall. As opposed to municipal water supplies, water from wells is often untreated; instead the well is regularly tested for the presence of coliform bacteria. Contamination in this case would occur without warning and the water could test clean until the next storm. Microbial treatment of source water can provide additional protection from unforeseen contamination.

Safeguarding against microbial contamination

Microbes of concern in the food, beverage and dairy industries are found in three broad “environments”: In water, on surfaces and in the ambient air or atmosphere. Microbial control in each of these environments requires different treatment technologies. Unclean or untreated surfaces and crevices can serve as a reservoir for growth, resulting in ongoing contamination and potentially tainted product. General plant hygiene and cleaning practices are a first line of defense against microbial contamination. Water and ingredient streams should be periodically checked for microbial contamination. Water heaters set at too low of a temperature can harbor microbial growth. Surfaces should regularly be cleaned and treated to inhibit microbial growth. Air handling equipment and filtration elements should be frequently checked for cleanliness and potentially fitted with microbial control elements.

Water is an integral component in cheese production as an ingredient, as the working fluid in heating and cooling operations, for cleaning equipment and for rinsing products and packages. Microbial contamination in water has the potential to affect the final product at multiple points, so particular care is warranted. Table 3 contains a list of several possible treatment technologies used for the disinfection of water.

Chemical treatment

Of microbial water treatment technologies, thermal and chemical disinfection are the most widely used for the treatment of drinking and other potable waters. Chemical disinfection, almost exclusively as chlorination with hypochlorous acid or salts thereof, is widely used for municipal treatment as it provides a long-lasting residual disinfection (water safety is maintained to the tap). Chlorine generation is a massive industrial process, so costs are low relative to more advanced chemical treatments like ozone. Chlorine damages cellular structures through oxidation thereby inactivating microorganisms. Disinfection with chlorine is surprisingly slow, potentially requiring several minutes to several hours of contact time at normal concentrations to be completely effective. For example, 2 log inactivation of giardia cysts in 10º C water with a pH of 7 requires 75 minutes of contact time with water containing 1 mg/l free chlorine according to the EPA Guidance Manual on Disinfection Profiling and Benchmarking, while 3 log inactivation requires 112 minutes. This is acceptable where there is significant residence time in pipes or channels between the point of application and the point of consumption.

Chlorine is added to the water as one of many forms depending on the application and other requirements. It can be provided as powders, prills or pellets, in liquid solutions and as a compressed gas. It can also be generated on-site by electrochemical reactions in salt water. Independent of form, dose control is key to successful chlorine application. The chlorine dose required to adequately sterilize water can vary widely with changes in dissolved or suspended organic material, the presence of dissolved or particulate metals and the microbial load of the water stream.

Chlorine disinfection is strongly pH dependent; a high pH (basic conditions) converts the active hypochlorous acid to the less effective hypochlorite ion. Low pH causes the hypochlorous acid to revert to chlorine gas, which is emitted to the atmosphere. Sunlight, dissolved metallic species and particulate inorganic material can also catalyze the destruction of hypochlorous acid. Chlorine is a powerful oxidizer and can cause corrosion of equipment at high concentrations. The same reactions that result in antimicrobial activity can also interfere with normal food chemistry, impacting product quality. Chlorine reacts with organic materials present in the water to form disinfection byproducts like halocarbons and chloramines. Halocarbons and chloramines can be health hazards and can affect taste, odor or product quality. Additionally, there are reports of certain bacterial species (e.g., mycobacteria), bacteria in biofilms and spores being resistant to chlorine treatment.1

There are disinfecting chemicals as alternatives to chlorine but they are used far less frequently due to cost, safety considerations, lack of familiarity and/or their potential impact on product quality. If ammonia is added to a chlorinated water stream it reacts with free chlorine to form chloramines that are useful disinfectants. Chloramines are only effective at concentrations significantly higher than chlorine and with long contact times, but provide an exceptionally long-lived residual disinfecting benefit. Disinfection with ozone (O3) is increasing in popularity, especially for use in swimming pools, but does not provide the strong residual disinfection of chlorine or chloramine and must be generated on-site. Chlorine dioxide is an exceptional disinfecting agent but is explosive when not dissolved and cannot be shipped. It must be generated on site immediately prior to use. Preservatives (e.g., bactericides and bacteristats) as food additives may have application in water disinfection, but they are expensive and there is little research into their use in treating water.

 Thermal treatment

Thermal disinfection is the oldest disinfection technology. Boiling water is sufficient to inactivate pathogens, although several hours of boiling may be necessary to treat bacterial endospores. High pressure autoclaves allow water to be heated above normal boiling (100º C or 212º F) and shorten disinfection times, but can require annual expensive safety testing (e.g., hydrostatic pressure tests) to ensure safe operation. Pasteurization heats the process flow to near boiling for a prescribed time and is the most widely used disinfection process in the food and beverage production industry. The lower temperature of pasteurization limits its effectiveness for destroying bacterial spores. Pasteurization is energy intensive due to the large specific heat capacity (energy required to heat a given volume of a given temperature) of water and the need to cool the water again prior to use. The high operational costs associated with pasteurization can be ameliorated with proper system design utilizing efficient heat exchangers. Microbial growth can be accompanied by the release of toxins (e.g., cyanotoxins in algal blooms), which persist even after the original microbial population is destroyed by pasteurization. These toxins are often implicated when there is an outbreak of foodborne illness of short duration unaccompanied by infection.

Ultraviolet irradiation

Ultraviolet (UV) disinfection is a widely used technique to inactivate microbes. The inactivation is caused by damaging a microbe’s DNA upon exposure to UV light, in particular UV-C light at primarily 240 to 270 nm wavelength. These microbes are not killed by exposure to UV, but rather they are rendered unable to reproduce and no longer infectious. The effectiveness of UV to inactivate a pathogen is proportional to the intensity of the UV light multiplied by the contact time (typically given as mJ×s/cm2 or mW/cm2). Water quality strongly affects the intensity of UV in an exponential manner. For example, if 90 percent of UV light is absorbed in the first centimeter of water, then only one percent of the initial intensity reaches a distance of two cm. The transparency of water to UV light is affected by calcium, alkalinity, hardness, iron content, manganese content, dissolved organic material and turbidity. The exponential loss of intensity to absorbance requires UV sterilizers to have either short optical paths or very high UV intensity to treat large flow rates.

Membrane processes

Microbes, although small in relation to human scales, are not infinitesimal. Filtration can be highly effective for providing microbially pure water. Nearly all microbes, except viruses, can be removed by size exclusion filtration with a 0.2 μm filter element; viruses can be removed by a 20 nm (0.02 μm) element, and an osmotic membrane can even remove dissolved salt and organic molecules. Filtration elements with small pore sizes rapidly clog in traditional filtration equipment and, therefore, membrane cross-flow filtration is typically used (Figure 1). Membrane filtration equipment costs do not economically scale down for small cheesemaking operations. Damaged membranes can allow untreated water to bypass the filter element and result in contamination. Bacterial growth in either cross-flow or dead-end filtration can result in filters clogging and decreased production.

Advanced oxidative processes

Several novel treatment methods are classified as advanced oxidative processes (AOPs). These techniques rely on the generation of hydroxyl radicals and other radical species capable of destroying cellular structures and breaking down organic chemicals. Photoelectrocatalytic oxidation (PECO) technology combines aspects of both UV radiation and chemical disinfection in a single device where high intensity UV light and a small electric potential are used to activate a solid nanostructured catalyst. In water with even minimal salinity, hydroxyl radicals oxidize chloride ion to generate chlorine, providing an additional germicidal method of action. This generated chlorine is quickly converted into further hydroxyl radicals by the action of the UV, resulting in hydroxyl radical formation in the bulk water and preventing residual chlorine from being produced by the system. The generated radicals are substantially stronger oxidizers than chlorine, so shorter contact times are required to damage critical microbial structures. The multiple disinfection mechanisms provide broad-spectrum control of microbes including yeast, mold, viruses and spores that might prove resistant to any one individual inactivation mechanism.

These oxidizing species also break down organic contaminants and toxins, such as emerging contaminants of concern, traditional water treatment technologies are unable to remove. Contaminants include pesticides, pharmaceuticals, hormones, endocrine disrupting compounds, plastic/polymer breakdown products, chlorinated solvents and gasoline additives that can leach into groundwater sources.



  1. P. A. Pelletier, G. C. du Moulin and K. D. Stottmeier, “Mycobacteria in Public Water Supplies: Comparative Resistance to Chlorine,” Microbiological Sciences 5, No. 5 (May 1988): 147–48.

Dr. Ramsey Kropp, Ph.D., chief scientist of AquaMost Inc., is an environmental chemist with a focus in water and air treatment, particularly the removal of pathogens and contaminants employing nanomaterials and advanced oxidative processes (AOPs) including photo- and photoelectro-catalytic heterogeneous catalysis, ozonolysis, UV sterilization and electrostatic precipitation.


Table 1: Microbes of concern in cheese manufacturing

Type of spoilage


Main microbe involved

Premature swelling Spongy, swollen cheese

Coliform bacteria



E. Coli

Late swelling Butanoic acid fermentation, gas formation Clostridium tyrobutyrium

C. butyricium

C. sporogene

Bitter taste Unpleasant taste Proteolytic enzymes present, disturbed ripening
Foreign mold Mold growth on cheese surface, mycotoxin formation Penicillium




Formation of holes Outsized holes due to gas formation Propion acid bacteria

Lactic acid bacteria

Discoloration Orange to red discoloration of cheese or brine Pigment forming bacteria (e.g. Micrococcus)
Table 2: Microbial contaminants in untreated domestic wastewater


Table 3: Microbial treatment technologies

Treatment technology



Chemical disinfectants (chlorine, chloramines, ozone, bactericides) Moderate initial cost, potentially results in complete disinfection Requires accurate dosing and tailoring to microbial species, potential exposure hazard, can affect food quality
Thermal disinfection (pasteurization or boiling) Historically most widely used technique, equipment typically already in place Energy intensive and requires significant cycle time, many microbial species surprisingly resistant to thermal shocks, can affect product quality and nutritional content
Ultraviolet radiation Widely used, low operating cost Effectiveness decreases in turbid/UV absorbing water, expensive equipment, can produce off flavors in fatty products
Membrane filtration (micro-, ultra-, and nano-filtrations) and reverse osmosis (RO) Highly effective, Moderate operating cost, no effect on taste High capital expense, requires occasional membrane replacement, does not scale down well


Figure 1: Cross-flow and dead-end membrane filtration