I’ll admit it. I’m fascinated by biofilms. These slimy bacterial cities are equal parts fascinating and challenging. I think they’re an incredible example of microbial teamwork: bacteria link up, build a little fortress of goo, and start passing DNA to each other like notes in class. One of them picks up a resistance gene, and suddenly the whole colony is impervious to your cleaner. That’s why it’s so important to periodically “shock” your lines and equipment with alternating alkaline and acid washes. Once a month is a good baseline, but we’ll get into that in another post. First, let’s talk about what these things really are, how they work, and why they’re a big deal for milk quality, udder health, and anyone who owns a bulk tank or milk bucket.
Biofilms are communities of microorganisms attached to a surface and encased in a self-produced matrix of extracellular polymeric substances (EPS). This slime-like layer helps them stick to equipment, resist sanitizers, and persist even when conditions are harsh. According to Weber et al. (2019), biofilms in milking machines develop quickly. Bacteria began forming on stainless steel within 48 hours of exposure. That means even if you clean after every milking, resilient cells may still be hanging on and rebuilding. By the time you get to your lines for the next milking, they could have built a metropolis!
Once established, biofilms can cause more than just a gross residue. They harbor spoilage organisms like Pseudomonas and Bacillus, both of which secrete heat-resistant enzymes that can survive pasteurization and reduce milk shelf life. More worryingly, pathogens like Listeria monocytogenes and mastitis-causing Staphylococcus species can lurk within the biofilm. In the Weber study, researchers detected Listeria DNA on milking equipment despite cleaning protocols. That’s a red flag for both animal health and consumer safety.
One reason biofilms are so tough to remove is that the bacteria inside are often metabolically dormant and shielded from chemical cleaners. Studies published in the Journal of Dairy Science and Frontiers in Microbiology show that biofilms shift microbial populations over time, often favoring species like Acinetobacter, Stenotrophomonas, and Microbacterium. These are not your average passive passengers; they’re active builders and defenders of their community, with strong adhesion and enzyme activity.
Another issue is that cleaning-in-place (CIP) systems, while convenient, don’t always target the spots with the heaviest biofilm loads. In both university and private farms studied by Weber et al., biofilms consistently formed at the outlet of the bulk tank and on the milking equipment retainers—places not always reached by automated cycles. Swabs from these areas were visibly loaded with debris and showed high diversity, including mastitis-linked bacteria.
What’s more, different surfaces play different roles. Plastic, for example, often has a rougher or more hydrophobic texture that helps biofilms get a foothold. Even if your pipeline is squeaky clean, an aging plastic inflow hose could be the weak link. And biofilm doesn’t stay in place. Bits can slough off and contaminate milk, animals, and any new surfaces they land on.
The good news? Biofilms are beatable. Consistent cleaning is a must, but alternating alkaline (like sodium hydroxide) and acid (like nitric or phosphoric) cleaners helps break down both organic matter and mineral buildup. Weber’s research found that systems alternating acid and alkaline washes between milkings had lower biofilm regrowth. More advanced dairy processors are now testing enzymatic cleaners or surfactant-boosted protocols to disrupt the biofilm matrix directly.
Lukewarm Rinse – Acid Cleaner – Alkaline Rinse – Dry
Immediate Lukewarm Rinse to get rid of milk residue. Lukewarm because if too hot, the milk proteins (casein) will cook onto the surface of your equipment and be very difficult to get off. Too cold and the milk fats will make a film that is hard to remove.
Hot Alkaline Wash (120F minimum) to remove fats, proteins, and minerals still clinging to equipment and to begin the process of breaking down biofilms. Alkaline solutions are better at dissolving fats and proteins. Manually clean and disassemble everything that milk touched every single time with brushes designed to clean specific equipment! Maintain the heat throughout cleaning.
Thorough Acid Rinse to rinse away all detergent residue which can interfere with the taste of your milk and with subsequent alkaline washes, but also to remove film that could encourage bacterial regrowth.
Warm Acid Rinse is very important to prevent mineral build up. Many people skip this step! Acid rinse should leave a surface Ph of about 3.4 to create an environment between milkings that is unfriendly to bacterial growth and to help prevent build up of milk stones (especially if you have hard water). Warm, not hot.
Completely Dry equipment. Bacteria loves moisture! They will just grow again between milkings. Let everything airdry completely by hanging for optimum air flow, don’t stack parts or leave hoses where droplets of water collect at bends. Disassemble parts to dry.
Watch for sneaky spots where biofilms hide like where surfaces are rough, cleaning solutions don’t flow well, gaskets with crevices, and complex valves.
Rotate your cleaners once a month.
Sanitize Again Before Milking to inactivate any surviving bacteria or kill bacteria that grew between milkings, especially if you only milk once per day or live where it is hot and humid.
Here, we use Star Sans Products. For washing we use PBW Alkaline Cleaner. For rinsing we use High Foaming Acid Anionic.
Follow all product labels.
Test Your Milk Regularly to verify your cleaning process works.
Stop with the bleach. Mixing concentrations is risky (unless you are testing with chlorine strips before using) and will degrade your equipment. Vinegar is not a quality disinfectant.
Prevention also matters. Regularly inspect and replace aging hoses, gaskets, or liners. Use single-use cloths on teats (I use dry baby wipes soaked in a chlorohexidine solution). Sanitize inflations and any part of the system that touches raw milk. And if you’re using glass jars or pails? Hand scrub them with alternating acid and base washes. If you see that rainbow sheen or smell something weird? Milk tastes off or spoils faster? You probably have a biofilm.
One last point to consider: biofilms are rarely just one species. They’re communities that are mixed and evolving. That’s part of what makes them so resilient and also so fascinating. Yuan, et al (2022) noted that some species within biofilms even suppress immune detection, giving pathogens cover to persist. So yes, I think biofilms, like so many things in nature that want to populate, are cool. But if you’re raising goats and milking them, you need to treat them like the microbial threat they are.
Relevance for Us
If you’re milking goats, biofilms are part of your daily life whether you see them or not. This research helps us identify problem areas like tank outlets and claw retainers, and it confirms the need for alternating cleaning agents. For small-scale dairies, this means upping your cleaning game even with simple equipment. For anyone making cheese, these residues can also impact flavor, quality, and safety. And from a herd health standpoint, reducing biofilm reduces your risk of environmental mastitis.
Quick Takeaways
- Biofilms form fast and resist standard cleaners
- They harbor spoilage and mastitis-causing bacteria
- Alkaline and acid cleaners used alternately can help disrupt biofilms
- Focus cleaning efforts on high-risk areas like tank valves and inflations
Citations
Desmousseaux, C., Guilbaud, M., Jard, G., Tormo, H., Oulahal, N., Hanin, A., Bourdonnais, E., Jha, P. K., & Laithier, C. (2025). Biofilms in the milking machine, from laboratory scale to on-farm results. Journal of Dairy Science, 0(0). https://doi.org/10.3168/jds.2024-25352
Friedlander, A., Nir, S., Reches, M., & Shemesh, M. (2019). Preventing biofilm formation by dairy-associated bacteria using peptide-coated surfaces. Frontiers in Microbiology, 10. https://doi.org/10.3389/fmicb.2019.01405
LaPointe, G., Wilson, T., Tarrah, A., Gagnon, M., & Roy, D. (2025). BIOFILM DAIRY FOODS REVIEW: Microbial community tracking from dairy farm to factory: Insights on biofilm management for enhanced food safety and quality. Journal of Dairy Science, 0(0). https://doi.org/10.3168/jds.2024-25397
Latorre, A. A., Oliva, R., Pugin, J., Estay, A., Nualart, F., Salazar, K., Garrido, N., & Muñoz, M. A. (2022). Biofilms in hoses utilized to divert colostrum and milk on dairy farms: A report exploring their potential role in herd health, milk quality, and public health. Frontiers in Veterinary Science, 9. https://doi.org/10.3389/fvets.2022.969455
Weber, M., Liedtke, J., Plattes, S., & Lipski, A. (2019). Bacterial community composition of biofilms in milking machines of two dairy farms assessed by a combination of culture-dependent and -independent methods. PLOS ONE, 14(9), e0222238. https://doi.org/10.1371/journal.pone.0222238
Yuan, L., Wang, H., Liu, W., Sadiq, F. A., & Zhao, Y. (2022). Editorial: Multi-species biofilms in the food industry. Frontiers in Microbiology, 13. https://doi.org/10.3389/fmicb.2022.1023428
Title Image from: Latorre, A. A., J. S. Van Kessel, J. S. Karns, M. J. Zurakowski, A. K. Pradhan, K. J. Boor, B. M. Jayarao, B. A. Houser, C. S. Daugherty, and Y. H. Schukken. “Biofilm in Milking Equipment on a Dairy Farm as a Potential Source of Bulk Tank Milk Contamination with Listeria Monocytogenes.” Journal of Dairy Science 93, no. 6 (2010): 2792–2802. https://doi.org/10.3168/jds.2009-2717.
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