Microbial Contamination: Understanding the Risks and How to Prevent Them
In fermentation, processes are primarily designed to target the growth of a single microorganism or a select group of microorganisms (i.e. microbial consortia) for either biomass or a metabolic product the microorganism(s) generates. Process parameters within fermentation are focused on pH control, presence or absence of oxygen (for both obligate and facultative microorganisms), temperature, and nutritional profiles that provide the optimal conditions for your desired microorganism to grow. But what happens when undesirable microorganisms infiltrate the process?
Understanding Microbial Contamination: What It Is and Why It Matters
Microbial contamination is when undesirable or unwanted microorganisms grow in a fermentation or bioprocess that competes with your production microorganism for resources, leading to negative impacts on your products, yield, and overall performance. These unwanted microorganisms impact every fermentation industry, including food and beverage¹˒² biocontrol³, probiotics⁴, pharmaceuticals⁵, and biofuels⁶˒⁷. These microorganisms are commonly associated with environmental sources (raw materials, soil, agricultural sources, or airborne microorganisms; commonly gram-positive bacteria; fungal contaminants)⁸˒⁹ or water or high moisture air systems (commonly gram-negative bacteria and fungal contaminants)⁹˒¹⁰.
The growth of these unwanted microorganisms has direct impacts on your production facility, increasing direct costs due to loss of raw materials, increased waste handling costs (wastewater treatment, shipping out contaminated materials), and increased production costs through reworking material. In some instances when contamination is reoccurring, operations will need to shut down to fully clean a facility, leading to production delays. This in turn leads to decreased revenue through lost sales and can impact the end user (e.g. damaged crops³) and can impact brand or company reputation if a recall is required¹¹˒¹². This can also lead to more scrutiny by regulatory authorities¹³.
Another significant impact within direct costs and brand impacts are the indirect costs of contamination, which take place in investigations and root cause analyses. Here, there can be a significant amount of time dedicated to understanding how contamination with unwanted microorganisms occurred and identifying the best means to overcome these issues.
Controlling Microbial Contamination
Cleaning and sanitation practices are the crux for preventing microbial contamination. In a fermentation facility, Clean in Place (CIP) practices are similar across industry segments but have subtle differences. The food and pharmaceutical fermentation industry typically perform single-pass cleanings, using their CIP chemistry (alkaline solutions, acid cleaners, sanitizers) once, to minimize cross contamination and provide greater levels of cleanliness. Multi-pass CIP systems are also a consideration if CIP chemistry can be used where cross contamination is not a factor, or if you have dedicated equipment or a dedicated facility making a single product type, like biofuel plants. Here, CIP chemistry can be cycled between equipment, ensuring concentrations are maintained allowing for multiple assets to be cleaned from the same alkaline (i.e. caustic) or acid CIP system.
Understanding the sterile boundary of your processing equipment is also a crucial aspect of controlling contaminating microorganisms. The sterile boundary are the points between which all materials are sterilized so no contaminating microbes survive, allowing for your production microorganisms to thrive, producing the materials you need. This encompasses the zone between assets in your facility, such as the valve and piping from your media sterilization equipment (e.g. Continuous Sterilizer, UHT, HTST equipment, etc.) to your cleaning, steam sterilized seed tank or fermentor, as well as the valves and lines leading to downstream processing.
These kinds of programs, in general, are designed to ensure cleanliness and sanitation of your facility, but some unwanted microorganisms are quite robust. If a contamination event were to occur, and CIP is performed, what do you do when recurrent contamination happens? Is your CIP adequate to remove biofilms that form on the piping of your facility? Are you thoroughly cleaning your sterile boundary? Are you using an optimal concentration for your single or multi-pass CIP system? Have you steamed at the optimal temperature, pressure, and time to ensure unwanted microorganisms do not persist?
How can Sensient BioNutrients Help?
Your Sensient BioNutrients Technical Services team is ready to support your facility! We have industry experts that have a track record of reducing and eliminating microbial contamination events in a wide variety of fermentation facilities. Our experts can review your CIP program, evaluate the sterile boundaries of your process, and help align on chemistry used to ensure optimal cleaning, sanitation, and sterilization! Reach out to your Sensient BioNutrients Account Manager to learn more today!
Sources
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² Zavišić, G. et al. 2024. Microbial contamination of food: Probiotics and Postbiotics as Potential Biopreservatives. Foods, 13; 2487: https://doi.org/10.3390/foods13162487.
³ Microbial Contamination Prevention and Quality management in the Manufacture of Agricultural Biologics: Guidelines and Best Practices. CropLife International. 2024.
⁴ Skowron, K. et al. 2022. Two faces of fermented foods – The benefits and threats of its consumption. Frontiers in Microbiology, 13; 845166: https://doi.org/10.3389/fmicb.2022.845166.
⁵ Wintzingerode, F. V., 2017. Biologics Production: Impact of bioburden contaminations of non-sterile process intermediates on patient safety and product quality. American Pharmaceutical Review. https://www.americanpharmaceuticalreview.com/Featured-Articles/337286-Biologics-Production-Impact-of-Bioburden-Contaminations-of-Non-Sterile-Process-Intermediates-on-Patient-Safety-and-Product-Quality/
⁶ Seo, S., et al. 2020. Anti-contamination strategies for yeast fermentation. Microorganisms, 8; 274: https://doi.org/10.3390/microorganisms8020274.
⁷ Brexo, . P., and A. S. Sant’Ana. 2017. Impact and significance of microbial contamination during fermentation for bioethanol production. Renewable and Sustainable Energy Reviews 73, 423-434.
⁸ Lorenzo, J. M. et al. Chapter 3: “Main groups of microorganisms of relevance for food safety and stability.” Innovative Technologies for Food Preservation. http://dx.doi.org/10.1016/B978-0-12-811031-7.00003-0.
⁹ Vijayakumar, R. and T. Sandle. 2011. A review of fungal contamination in pharmaceutical products and phenotypic identification of contaminants by conventional methods. European Journal of Parenteral and Pharmaceutical Sciences, 17(1): 4-19.
¹¹ “DermaRite Industries Expands Voluntary Nationwide Recall…” https://www.fda.gov/safety/recalls-market-withdrawals-safety-alerts/dermarite-industries-expands-voluntary-nationwide-recall-due-potential-burkholderia-cepacia#recall-announcement
¹² U.S. Microbiology and Bacterial Culture Media Market (2025-2030). Grand View Research. https://www.grandviewresearch.com/industry-analysis/us-microbiology-bacterial-culture-media-market-report#:~:text=The%20upward%20trend%20in%20product,quality%2C%20reliable%20culture%20media%20products.
¹³ Patel, R. et al. 2024. A retrospective regulatory analysis of FDA recalls carried out by pharmaceutical companies from 2012 to 2023. Drug Discovery Today 29(6): https://doi.org/10.1016/j.drudis.2024.103993.
