The dairy industry must ensure the safety and quality of its products throughout their shelf life, while modern consumers demand food with simple, understandable ingredient lists. Ingredients with chemical-sounding names are often perceived as concerning. The concept of “clean label” refers to products with simple, transparent ingredients, free from complex and synthetic names. Numerous studies have shown that most consumers trust clean-label products more and are even willing to pay extra for natural ingredients. The main challenge for manufacturers is to strike a balance between safety, health, extended shelf life, and the use of natural alternatives instead of chemical additives.
This article aims to explore the clean-label concept and introduce effective ingredients for preserving dairy products.
Definition of “Clean Label”
The definition of “clean label” is not entirely consistent between consumers and the food industry and is still evolving. However, both parties agree on the importance of naturalness and minimal chemical processing. Foods labeled as organic, non-GMO, hormone- and antibiotic-free, plant-based, or packaged in eco-friendly materials are also typically considered clean-label.

From the Consumer Perspective: Consumers want to feel comfortable when purchasing food. Clean labels allow this by listing familiar, natural, and minimally processed ingredients. Synthetic or bioengineered ingredients are seen as processed and unfamiliar, often avoided due to safety concerns.
From the Industry Perspective: The food industry considers identifiable ingredients those with simple names. Clean-label products often have shorter ingredient lists, and food companies are increasingly reformulating their products using natural ingredients.
The Need for Natural Antimicrobials in Dairy Products
In the dairy industry, preservatives are used for various reasons, including enhancing safety, quality, and nutritional value, and extending shelf life by inhibiting spoilage bacteria, yeasts, and molds.
Preventing the growth of pathogenic bacteria is a major reason for applying preventive measures in dairy. According to the CDC, nearly all dairy-related illnesses in the U.S. are linked to raw milk. Thermophilic bacterial spores like Bacillus cereus can also survive pasteurization and cause spoilage. Additionally, although dairy products are less prone to fungal spoilage due to their acidic pH, contamination by molds such as Aspergillus and Penicillium may still occur.
Given their vital role, the use of antimicrobials in dairy is under strict regulation to ensure product safety. Preservatives such as natamycin, potassium sorbate, and certain organic acids are approved for dairy use but must comply with specific usage guidelines.
Clean-Label Antimicrobials for Use in Dairy Products
- Food Cultures
Microbial cultures, especially in dairy, not only affect flavor and texture but also improve nutritional value, safety, and shelf life. Lactic acid bacteria (LAB), in particular, play a crucial role in fermentation, which helps both in taste enhancement and product preservation due to their antimicrobial properties.
1.1 Protective Cultures
Microbial cultures specifically selected for producing antimicrobial metabolites without altering the food’s physicochemical, sensory, or nutritional attributes are known as protective cultures and align with clean-label trends. LAB such as species of Lactococcus, Lactobacillus, Leuconostoc, Pediococcus, and Streptococcus are commonly used in dairy to control pathogens.
1.2 Antimicrobial Compounds in Protective Cultures and Fermented Products
The main antimicrobial agents in protective cultures and fermented products are organic acids and bacteriocins. Organic acids such as lactic, acetic, and propionic acids are particularly effective by disrupting microbial cell growth through internal pH reduction.
1.2.1 Organic Acids
LAB produce a variety of organic acids during fermentation. Their efficacy depends on the target microbe, concentration, and incubation time and temperature.
Although pure organic acids are not considered clean-label due to their chemical nature, they can be sourced naturally. Lemon juice (citric and malic acid) and vinegar (acetic acid) are potential natural preservatives.

1.2.2 Bacteriocins
Bacteriocins are antimicrobial peptides produced by bacteria and have been present in fermented foods like cheese and yogurt for centuries. Over 230 LAB-derived bacteriocins have been identified, mostly effective against Gram-positive bacteria.
Nisin, produced by Lactococcus lactis, is approved in over 50 countries for dairy, meat products, and ready-to-eat foods and is the only commercially used bacteriocin in the U.S. It works by forming pores in bacterial membranes, leading to cell death. Though it usually does not affect taste or texture, some studies note yeasty flavors or watery textures in nisin-containing products.
Ideal bacteriocins should be safe for humans, effective against pathogens and spoilage organisms, heat- and pH-stable, and neutral in sensory impact. While some consumers may not view bacteriocins as clean-label, they are relatively well accepted in the U.S. and Europe.
1.3 Fermented Products Derived from LAB
Instead of using live bacteria, another approach is using their fermented products. These “ferments” contain organic acids and bacteriocins produced during bacterial fermentation and function similarly to protective cultures. Cultured sugar products are a common example.
Ferments offer better control over antimicrobial activity and timing compared to live cultures.
1.4 Fermented Products from Yeasts and Filamentous Fungi
Fungi, including yeasts and molds, have been used in food production for centuries and play valuable roles in flavor, texture, and preservation. Common species like Aspergillus niger, Aspergillus oryzae, and Saccharomyces cerevisiae are GRAS (Generally Recognized As Safe).
Yeasts such as Saccharomyces are essential in fermentations like alcohol production in kefir or curdling milk in cheese. Some yeasts also display antimicrobial properties. Fungal fermentates—compounds produced during fermentation—are being studied as non-chemical preservatives to extend shelf life and improve sensory and nutritional quality. Research on their safety and efficacy, especially in dairy, is ongoing.
- Plant-Based Compounds and Natural Essential Oils
Natural essential oils are volatile aromatic compounds extracted from plants and possess strong antimicrobial activity due to phenolic and terpenoid constituents. Many are recognized as safe (GRAS) by the U.S. FDA.
Essential oils such as thyme, oregano, black cumin, cinnamon, cumin, and rosemary can inhibit the growth of bacteria and fungi in dairy products like cheese and butter, mainly by disrupting microbial membranes.
Studies show that adding thyme oil to Feta cheese and black cumin oil to soft cheese or butter inhibits Listeria monocytogenes and E. coli, respectively.
However, challenges such as interactions with fats, proteins, and carbohydrates in food may reduce their effectiveness or cause off-flavors at higher concentrations. Research continues into methods like nanoencapsulation to enhance their efficacy.
- Bacteriophages
Bacteriophages are viruses that infect and, under specific conditions, kill bacteria. Phage biocontrol involves using specific phages to target harmful or spoilage bacteria without affecting beneficial ones.
Environmental factors such as heat, salt, and bacteriocins can activate dormant phages, triggering the lytic cycle to destroy bacterial host cells.
The FDA has approved some phages, including Listeria-specific ones, as GRAS food additives.
Studies have shown that phages can be effective in dairy products.
Studies have shown that bacteriophages can be effective in dairy products. For example, S. aureus phages have been successful in inhibiting the growth of this bacterium in pasteurized and UHT milk. Additionally, a significant reduction of Salmonella enteritidis and Shigella in milk and yogurt has been reported following the addition of phages. However, factors such as high pH, low storage temperatures, high mineral content, and large bacterial populations can interfere with phage activity in food products.
Although numerous studies have demonstrated the efficacy and cost-effectiveness of phages in controlling foodborne pathogens, fewer investigations have focused on their use as preservatives in dairy products. This caution stems from the dairy industry’s concern about fermentation disruption and financial losses caused by phage contamination of starter cultures. Nevertheless, in countries like the United States, Canada, Australia, and within the European Union, bacteriophage-based products have been approved for clean label processing.

- Antimicrobial Agents of Animal Origin
Antimicrobial agents of animal origin are primarily derived from vertebrates. These compounds include lysozyme, lactoferrin, chitosan, lactoperoxidase, and ovotransferrin. Extensive research has confirmed their effectiveness against foodborne pathogens and spoilage microorganisms.
The following section discusses the mechanisms of action of natural antimicrobial compounds found in dairy products, with a particular focus on lysozyme and milk-derived peptides.
4.1 Lysozyme
Lysozyme is a small protein with natural antimicrobial properties found in various sources such as milk, egg whites, and saliva. The production of lysozyme in milk increases with high-temperature, short-time pasteurization methods, while it decreases under low-temperature, long-time processes. The U.S. Food and Drug Administration (FDA) has approved egg-white-derived lysozyme as a GRAS (Generally Recognized as Safe) additive for preventing late blowing in cheese caused by Clostridium tyrobutyricum.
Lysozyme’s antimicrobial effect is due to its ability to break the β-1,4 linkage in bacterial cell walls, leading to cell death. Gram-negative bacteria are generally more resistant to lysozyme because of their lipopolysaccharide layer, whereas egg white lysozyme has shown efficacy against certain Gram-positive bacteria. Studies have shown that lysozyme use in freshly pasteurized milk can reduce bacterial counts by up to 99% and preserve the milk’s sensory qualities for a longer period. However, temperatures above 85°C significantly reduce lysozyme’s activity and stability. Techniques like high-intensity pulsed electric field treatment, when used in combination with lysozyme, can enhance its antimicrobial effect without drastically altering the milk’s sensory properties.
4.2 Peptides Derived from Casein and Whey Proteins
Extensive research has been conducted on the functional properties of bioactive compounds in dairy products. While cow’s milk proteins—casein and whey—are not inherently antimicrobial, they can produce bioactive peptides with antimicrobial properties during hydrolysis. These peptides disrupt bacterial cell membranes, leading to cell lysis.
Peptides derived from caseins have shown activity against bacteria such as S. aureus, B. subtilis, S. pyogenes, and Diplococcus pneumoniae. Among whey-derived peptides, α-lactalbumin, β-lactoglobulin, lactoferrin, and lactoferricin have been identified. In one study, the addition of lactoferrin to cheese led to reduced growth of bacteria, yeasts, and molds at both room and refrigerated temperatures. Moreover, increasing the concentration of lactoferrin reduced the cheese’s hardness, cohesiveness, elasticity, and chewiness, without negatively affecting overall consumer acceptance.
Milk-derived bioactive peptides are gaining attention as natural preservatives. Bovine lactoferrin, for instance, has been approved for use in products such as infant formula. Because of their natural origin, peptides derived from casein and whey fall into the category of natural additives and can serve as safe and effective alternatives to synthetic preservatives.
Conclusion
Many natural antimicrobial compounds are recognizable to consumers and can serve as alternatives to synthetic preservatives in dairy products. However, producing clean label dairy products poses several challenges.
Consumer awareness has led to increased demand for high-quality foods with clear and understandable ingredient lists. A major limitation of natural antimicrobials is the lack of standardized regulations. New antimicrobial compounds intended for food use typically require costly safety and efficacy testing. In some cases, producers use a combination of methods—such as thermal or non-thermal processes alongside conventional preservatives—to control microbial growth, but the stability of natural preservatives under such processes remains unclear.
Some of these compounds may be produced more cost-effectively or with improved functionality using genetically modified organisms, but this approach conflicts with clean label principles. From an opportunity standpoint, clean label products can enhance brand transparency and build consumer trust. However, replacing synthetic additives may alter the product’s physicochemical, sensory, or nutritional characteristics.
These compounds also tend to be more expensive and may have a shorter shelf life than synthetic alternatives. Emerging non-thermal technologies, such as high-pressure processing, may serve as clean label alternatives to traditional methods and could compete with natural preservatives. To strike a balance between consumer acceptance and production goals in using new clean label additives, a middle-ground approach is needed—one that maintains food safety without compromise.
Reference:
Choi, Dasol et al. “Comprehensive review of clean-label antimicrobials used in dairy products.” Comprehensive reviews in food science and food safety vol. 23,1 (2024): e13263. DOI: 10.1111/1541-4337.13263




