Fighting Foodborne Pathogens with Natural Antimicrobials

the World Health Organization traced back ~150 cases of multidrug-resistant Salmonella Typhimurium infection in 11 countries to chocolate produced in Belgium, resulting in one of the largest chocolate product recalls to date. This is not an isolated incident. Every year, about 1 in 10 people fall prey to foodborne illnesses, as a result of food contaminated with harmful microorganisms or chemical substances. Contamination can occur at different stages of food preparation-processing, storage, distribution and/or handling-and is a severe burden on public health and the economy. Hence, preserving food is important for ensuring food safety and reducing wastage.

The food industry has now started exploring natural alternatives for preserving food to reduce the dependency on chemical preservatives, some of which are linked to obesity and metabolic syndrome. Specifically, natural antimicrobials produced by plants and microorganisms like bacteria and fungi can kill food-borne pathogens like Salmonella Typhimurium, Escherichia coli, Listeria monocytogenes and Clostridium botulinum and also food spoilage bacteria like Brochothrix thermosphacta, Lactobacillus spp., Bacillus spp. and Weissella spp., among others. Foodborne pathogens and spoilage microbes pose a serious health concern for consumers and destroy the appearance, texture and sensory characteristics of the food, affecting the food industry and consumers alike.

Essential Oils-Essential Plant-Based Antimicrobials

Herbs like oregano, thyme and rosemary are not only great flavoring options, but they also possess a treasure trove of antimicrobial potential against pathogens. Plants produce aromatic and volatile liquids called essential oils that have a wide spectrum of antimicrobial activity towards both gram-positive and gram-negative pathogens. Essential oils are important arsenals of plants’ defense against pathogenic bacteria, fungi and insects, and the food industry is leveraging this knowledge to ward off food-borne pathogens.

Antimicrobial properties of essential oils can be mostly attributed to the presence of phenolic compounds like carvacrol, thymol and eugenol. The mechanism of action of these antimicrobial compounds is not understood completely, but evidence suggests that phenolic compounds can make the bacterial cell membrane permeable, release intracellular contents or may interfere with membrane function by interacting with bacterial membrane proteins.

In addition to possessing antimicrobial activity, essential oils of different herbs and spices like oregano, thyme, cloves, rosemary and turmeric are also safe for human consumption. They are considered Generally Regarded As Safe (GRAS) by the U.S. Food and Drug Administration (FDA). Their antimicrobial activity against food-borne pathogens or spoilage bacteria depends on a number of factors-their concentration and method of extraction, as well as the pH and temperature of food, to name a few. In a 2019 study, researchers showed that a low dose of tree tea essential oil (1.5% volume by weight) inhibits L. monocytogenes growth in ground beef. Another study in the same year demonstrated that the essential oil of garlic inhibited the growth of fungi Aspergillus niger and Aspergillus flavus in plum fruit.

Bacteriocins-Weapons of Bacterial Warfare

Just like essential oils help plants fight pathogens, some bacteria produce small peptides with antimicrobial properties against closely related bacteria, which becomes advantageous when competing for resources in shared environments. These small peptides are called bacteriocins and help bacteria to establish their niche in the ecosystem. Bacteriocins are considered safe for human use as they are easily degraded by enzymes in the human gastrointestinal tract. Many of them are produced by bacteria belonging to Lactic Acid Bacteria (LAB) group that have a GRAS status. They can be used for food preservation in different ways-as purified products or by addition of bacteriocin-producing bacteria directly to the food.

 Application of lactic acid bacteria and bacteriocins in meat products.
Application of lactic acid bacteria and bacteriocins in meat products.

One of the most well-studied bacteriocins is nisin, an antimicrobial peptide produced by Lactococcus and Streptococcus species. As of now, nisin is the only bacteriocin licensed by the U.S. FDA as a food preservative. Nisin inhibits bacterial growth by forming pores in cell membranes and blocking cell wall synthesis. It is used in many foods including dairy, meat and juices, either alone or in combination with other biopreservatives. For instance, nisin is used in the cheese industry to control the growth of Clostridium spp. and in the meat industry to reduce levels of L. monocytogenes. However, more research and clinical studies to test the immunogenicity and toxicity of other bacteriocins are needed for approval by regulatory authorities.

Delivering Antimicrobials in Nanocapsules

While the idea of using essential oils extracted from herbs and spices and bacteriocins from LAB sounds great in theory, several factors limit practical applications. For example, the intense aroma (and flavor) of essential oils in food may not please everyone. Additionally, both essential oils and bacteriocins suffer from poor solubility and stability, reducing their efficacy.

Schematic representation of bacteriocin encapsulation with liposome for antibacterial activity.
Schematic representation of bacteriocin encapsulation with liposome for antibacterial activity.

Technology to overcome these limitations is being investigated. One possibility is to deliver these antimicrobial sources by encapsulating them in nanoparticles, which allow them to remain stable in food items under different pH and temperatures. Such a system would ensure a slow and gradual release of antimicrobials during the shelf life of the food source, ensuring food preservation for longer durations. This is especially useful for controlled application of essential oils that may otherwise modify the sensory properties of the food.

Scientists are researching several biopolymers (e.g., chitosan, dextran, starch and alginate) that are non-toxic and eco-friendly to encapsulate essential oils and bacteriocins with promising results. For instance, nanoemulsions of clove essential oil in chitosan demonstrated improved antifungal activity against A. niger and encapsulating nisin with alginate/resistant starch increased its efficiency in controlling Clostridium growth in cheddar cheese, compared to nisin treatment alone.

Delivering Antimicrobials in Edible Coatings and Packaging

If you have ever picked fruit on a farm, you will easily spot the difference between the fruit growing on trees and that which is sold in a grocery store. Often, the latter is treated with food-grade wax or edible films that give fruits their glossy appearance. The wax can be made up of chemicals or natural sources that protect the produce from moisture and spoilage.

Incorporating active ingredients like antimicrobials in food packaging can hit 2 targets with 1 stone-inhibiting the growth of spoilage microbes and extending the shelf-life of fresh produce. For instance, essential oils of oregano and/or thyme in soy protein isolate films reduced the populations of Pseudomonas spp. and coliforms in fresh ground beef patties, and chitosan coating, combined with nisin and a synthetic surfactant lauric arginate, reduced the growth of L. monocytogenes in sliced turkey deli meat.

Application of essential oils in food packaging.
Application of essential oils in food packaging.

In June 2022, scientists developed a low-cost and high-throughput food packaging system that wraps antimicrobial fibers around the food like a spiderweb. The system uses pullulan, a naturally occurring polysaccharide as the fibroid backbone, which is mixed with natural antimicrobials like nisin, citric acid and thyme oil. Using this system, scientists showed that avocados wrapped with antimicrobial pullulan fibers had longer shelf-life, better moisture retention and less natural microflora, compared to uncoated avocados. The wrapping is biodegradable and can be easily washed away, making it a promising method to package perishable products.

Concerns Around Antimicrobial Resistance

When deploying any antimicrobial in the field, it is essential to address issues associated with the emergence of resistant pathogens. We don’t know much about the development of antimicrobial resistance in foodborne pathogens or spoilage microbes when essential oils and bacteriocins are used as food preservatives.

However, there are some lab-based studies that reveal why some bacteria are resistant to certain types of bacteriocins or essential oils. For instance, an S. enterica outbreak in 2007 was traced backed to fresh basil leaves. Basil leaves are rich in phenolic compounds with antimicrobial activities, so this came as a surprise. Studies in the lab showed that S. enterica was able to develop resistance to active ingredient linalool in basil. Other studies have shown that some bacterial strains of B. subtilis and L. monocytogenes that are resistant to nisin have higher levels of ABC transporters that expel nisin from the membrane and make bacteria immune.

It is critical to understand the mechanism of resistance to help minimize the emergence of resistance in the long term. Diving into these mechanisms, may reveal possible avenues to chemically synthesize derivatives of natural antimicrobials and/or use a combination of antimicrobials to overcome resistance.

Future Considerations For Natural Antimicrobials

As the demand for fresh produce rises among health-conscious consumers, so does the need to prevent their spoilage by pathogenic microbes. Natural antimicrobials offer a safer alternative to chemical preservatives for food preservation. However, some concerns need to be addressed.

One major concern is determining the concentration of natural antimicrobials in food. Many studies addressing the effect of essential oils and bacteriocins on pathogenic microbes are performed in vitro on isolated bacterial species. However, they don’t translate well when these antimicrobials are added to food items, presumably due to complex underlying interactions between the antimicrobials, the chemical structure of the food and the environment. Often, a higher concentration of antimicrobial is needed in food compared to in vitro studies, and regulatory authorities need to ensure these concentrations remain safe for human health.

Methods of application and delivery of antimicrobials also need to be optimized for different foods and different kinds of pathogens, without disturbing the sensory characteristics of the produce. Some potential solutions are delivering natural antimicrobials in nanoencapsulations and eco-friendly coatings, as well as testing the synergistic efficacy of a combination of antimicrobials.

Most importantly, the food industry and regulatory authorities have a moral obligation to actively involve consumers in the process in a transparent manner. Additional studies are needed to ensure that these systems preserve the chemical, biological and sensory properties of the food, without causing any harmful side effects to consumers’ health.


Interested in learning what microbes span the clinical lab…and your grocery list? This article details 3 microorganisms that, while opportunistic and capable of causing disease, are also being used for important functions, including development of food products.

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