E. coli in Dairy and Kefir: A Farmer’s Guide to Safe, Healthy Milk

by | Sep 10, 2025 | Uncategorized | 0 comments

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E. coli is a common bacterium that lives in the intestines of humans and animals. Most strains are harmless, but some can cause serious illness. As farmers, we want to educate our community about where Escherichia coli (E. coli) comes from, how it can affect health, and what we do on our farm to keep our milk safe. In this article, we answer key questions about E. coli in dairy, pasteurization methods, and the benefits of kefir fermentation. We also share how Secret Lands Farm uses traditional practices to be transparent and ensure our grass-fed kefir and cheeses are both nutritious and safe.

What Is E. coli, and Where Is It Found?

E. coli is a type of bacteria found nearly everywhere – in soil, water, food, and in the intestines of people and animals. In fact, E. coli is a regular part of healthy gut flora in humans and many animals. It helps digest food and even produces certain vitamins in our intestines. You, your family, and your pets naturally carry plenty of harmless E. coli in your bodies. However, harmful strains of E. coli also exist in the environment. These strains can come from the feces of animals and contaminate places where we live or play. 

For example, E. coli from animal droppings can get into farm soil or water sources. Pets that roam outdoors may pick up E. coli bacteria by stepping in or sniffing contaminated areas. People can encounter E. coli by touching animals at farms or petting zoos, or by swimming in contaminated water. 

Farm Visits and Hygiene Risks

Public health experts note that even visiting farms or petting animals can be a risk factor for E. coli infection if proper hygiene isn’t followed. This is why we always stress good handwashing after visiting the barn or handling animals. Primary sources of E. coli in food include certain high-risk foods. Dangerous strains like Shiga toxin-producing E. coli (STEC) often spread through undercooked ground beef, unwashed vegetables, and raw milk. 

In other words, you might find harmful E. coli in a burger that wasn’t cooked enough, on lettuce fertilized with manure, or in unpasteurized dairy products. These foods can carry E. coli from farm animals into your kitchen. According to the World Health Organization, the major reservoirs of the worst E. coli (such as the O157:H7 strain) are cattle. But other farm animals like sheep and goats are also significant sources. Even wildlife and pets can carry these bacteria. Studies have found that dogs and cats can be infected with E. coli O157 as well.

In summary, E. coli is all around us. It thrives in the guts of warm-blooded animals, which is why it ends up in our environment through feces. Families and pets can encounter this bacterium in everyday life – from eating or handling raw foods to touching contaminated surfaces or animals. The key is understanding which strains are harmful and how to avoid them. In the next section, we’ll look at what happens if a harmful E. coli does get into your body.

Health Consequences of E. coli Infection

Most E. coli strains are harmless, but if you ingest a disease-causing strain, it can make you sick. The effects can range from mild to very serious. A common outcome of infection is gastroenteritis – basically an upset stomach with diarrhea and cramps. Often, there is abdominal pain, and the diarrhea can become bloody in severe cases. You might also experience fever or vomiting for a few days. 

In healthy adults, these symptoms usually resolve on their own within about a week. It’s the body’s way of clearing out the unwanted bacteria. However, certain strains of E. coli produce powerful toxins that can cause more than just a stomach bug. One notorious example is E. coli O157:H7, which is classified as a Shiga toxin-producing E. coli (STEC). Infection with these strains can lead to a life-threatening complication called hemolytic uremic syndrome (HUS). 

Hemolytic Uremic Syndrome: A Serious Complication

HUS is a serious condition that causes kidney failure and blood cell destruction. Young children and the elderly are especially vulnerable to HUS and other severe outcomes. Experts estimate that up to 10% of people (mostly kids) who get a toxin-producing E. coli infection may develop HUS. HUS can require intensive care, and in the worst cases, it can be fatal. Even survivors might have lasting kidney damage. This is why public health warnings about E. coli outbreaks are taken so seriously.

Beyond gut illnesses, E. coli can affect other parts of the body if it gets in the wrong place. For example, E. coli from the gastrointestinal tract is the most common cause of urinary tract infections (UTIs), especially in women. If it enters the bloodstream, it can cause sepsis (a dangerous body-wide infection) or even meningitis in infants. In rare cases, certain E. coli strains can cause pneumonia. Essentially, while E. coli normally lives harmlessly in our intestines. If a harmful strain ends up where it shouldn’t (like our stomach, bladder, or blood), it can lead to serious illness. 

Key takeaway: Having E. coli in your body is normal – but having the wrong strain in the wrong place can be dangerous. Symptoms often start with diarrhea and stomach pain. If you ever notice bloody diarrhea or severe cramps after a suspected food exposure, it’s essential to seek medical care. Though most people recover fully, complications like kidney failure can occur in vulnerable individuals. Knowing this drives us as farmers to prevent harmful bacteria from ever reaching your plate.

How Modern Dairy Farms Eliminate Harmful Bacteria in Milk

One of the primary ways that harmful bacteria like E. coli can enter your body is through contaminated milk or dairy products. Decades ago, diseases from milk were far more common, but today, modern farms have effective methods to eliminate these dangers. The two main lines of defense are pasteurization and fermentation. We use both at our farm to ensure that milk is safe from harmful bacteria while preserving its goodness.

Pasteurization: Heating Milk to Kill Pathogens

Pasteurization is the process of heating milk to a specific temperature for a set time to kill pathogens. This practice became standard because raw milk (milk that hasn’t been heated) can harbor dangerous germs such as E. coli O157:H7, Salmonella, Listeria, and others. 

Louis Pasteur, the French scientist, invented this technique in the 19th century to make milk and wine safer. It’s been a public health game-changer for dairy. In Canada, for example, all milk sold to the public must be pasteurized by law. This law exists because it protects you, the consumer, from milk-borne illnesses that were once tragically common. 

How Pasteurization Kills Harmful Bacteria

During pasteurization, milk is typically heated to about 72°C for 15 seconds (or an equivalent method) and then rapidly cooled. This simple step destroys 99.9% of disease-causing bacteria in the milk. Notably, that includes the vegetative cells of E. coli (the form of the bacteria that can make us sick), which are killed by standard pasteurization. Even the most heat-resistant non-spore bacteria found in milk are eliminated at pasteurization temperatures. In plain terms, proper pasteurization makes milk safe from E. coli and other common pathogens. 

Crucially, pasteurization achieves this without significantly changing the milk’s nutrition. Research has shown that pasteurized milk remains rich in proteins, calcium, and vitamins, with only minimal losses of heat-sensitive vitamins. One Canadian resource notes that pasteurization destroys harmful bacteria like E. coli while maintaining milk’s nutritional value. 

Thanks to pasteurization (and better farm hygiene), milk went from causing 25% of all foodborne illnesses in 1938 to less than 1% today. That is a tremendous improvement in food safety. Because of these benefits, modern dairy farms pasteurize milk as a standard practice. 

At Secret Lands Farm, we take pasteurization very seriously for any milk we bottle or use fresh. We know it’s the most reliable way to protect our family and customers from invisible dangers. We’ll discuss the specific pasteurization method we use and its rationale in the next section.

Fermentation: Using Good Bacteria to Improve Safety

Besides heat treatment, another tool farms use is fermentation – harnessing beneficial microbes to crowd out the bad ones. Fermented dairy products like cheese and kefir are not just delicious; they are also generally safer from harmful bacteria due to the fermentation process. Here’s how it works: when we add kefir grains to milk and let it ferment, these friendly microbes consume the lactose (milk sugar) and produce lactic acid and other compounds. This causes the milk’s pH to drop (become more acidic) within hours. 

Fermentation Creates a Hostile Environment for Pathogens

Most harmful bacteria, including E. coli, do not grow well in high-acid, low-sugar conditions. The environment created by fermentation becomes hostile to pathogens. Essentially, the good bacteria outcompete or outright inhibit the growth of harmful bacteria. Take kefir as an example (we’ll discuss it in detail later). When milk is fermented into kefir, the resulting drink becomes so acidic that unwanted bacteria like E. coli simply cannot multiply in it. A recent study showed that fermenting milk into kefir achieved a similar log-reduction in E. coli as pasteurization does. In other words, fermentation can dramatically reduce the bacterial count, essentially sanitizing the product naturally. 

Traditional raw milk cheeses rely on this principle too: during aging, the combination of lactic acid, beneficial microbes, salt, and low moisture creates conditions where pathogens die off over time. For instance, hard cheeses made from raw milk are often required to be aged at least 60 days; by that time, studies have found that E. coli is usually not detectable in the cheese. Fermentation, along with proper salt and drying, is Mother Nature’s way of purifying the food. It’s important to note that fermentation is not a foolproof kill-step like pasteurization. It significantly suppresses harmful microbes but may not eliminate every single pathogen if the contamination is very high to begin with.

That’s why dairies still pasteurize when required by law or when making fresh products. But fermentation is a fantastic additional hurdle for bacteria. Modern farms use it to produce foods that are both safe and full of probiotics. At our farm, we embrace traditional fermentation methods in products like aged sheep cheese, yogurt, and kefir, because they add safety and health benefits. Next, we will explain how we combine these approaches at Secret Lands Farm, and why we chose our specific techniques.

Our Traditional Approach at Secret Lands Farm

At Secret Lands Farm, we pride ourselves on being as transparent as possible about our methods. We blend time-honored farming traditions with modern food safety science to ensure our dairy products are both safe and nourishing. In practice, this means we pasteurize our milk at a lower temperature for a longer time, and we also offer select raw fermented products (like aged cheeses and kefir for pets) made with the utmost care. We even share videos of our cheese and kefir making so you can see exactly how it’s done. You’re also welcome to visit us for a farm tour, meet our happy, healthy sheep, and even stay for a brunch or a cheese tasting. We want you to feel confident in what you feed your family – and that starts with understanding how we handle our milk.

Low-Temperature Pasteurization (63 °C) to Protect Nutrients

For almost all our dairy (milk, fresh cheeses, yogurt, etc.), we use pasteurized milk. However, unlike large industrial dairies that often use high-temperature short-time pasteurization, we use a gentler method known as low-temperature long-time (LTLT) pasteurization. We heat our milk to 63 °C and hold it there for 30 minutes, then cool it quickly. This is sometimes referred to as vat pasteurization, an old-fashioned but effective technique. 

Why did we choose 63 °C? Because we believe it offers the best of both worlds – it kills harmful bacteria in milk while preserving the milk’s “soul,” its nutritional and flavor profile. Science supports this: pasteurization done correctly destroys pathogens like E. coli and Salmonella but maintains the nutritional value of the milk. By avoiding extremely high heat, we feel we retain more of the delicate proteins, enzymes, and vitamins that make farm-fresh milk so special. There is a lot of debate out there (and even within the dairy industry) about the “right” pasteurization temperature. Some argue that higher heat is more efficient, while others point out that ultra-high temperatures can overcook the milk and alter its taste. After reviewing the research and considering our traditional approach, we decided on 63 °C pasteurization as our standard. 

Safe Milk That Preserves Natural Goodness

It’s actually the original method recommended by Louis Pasteur and mandated in some of the earliest dairy laws. We trust it because it’s thoroughly proven – it has been used for generations to make milk safe. We also appreciate that it is a slower process; it aligns with our philosophy of slow food and careful craftsmanship. 

By heating milk in small batches, we keep a close eye on quality at every step. The result is milk that we are proud of: safe, rich in flavor, and packed with nutrients. Lab tests show that this pasteurization temperature still eliminates the harmful bacteria. For example, E. coli O157 and other vegetative pathogens cannot survive 63 °C for the required time. Meanwhile, the milk retains its lovely creamline and many of the raw characteristics that our customers love. It’s the milk we drink with our own family every day. We want you to have the peace of mind that our dairy is free from dangerous germs, but still as close to nature as possible.

Raw Milk Cheeses and Kefir: Tradition Meets Safety

While we pasteurize most products, we do make a few traditional raw milk products. These include some of our long-aged raw sheep milk cheeses and our raw milk kefir for pets. We take additional precautions and apply rigorous standards to these because they are not pasteurized.

Let us explain why we offer them and how we ensure they’re safe. 

First, certain cheeses made from raw milk are prized for their complex flavor – a result of the natural flora in the milk. We produce raw milk cheeses only under very controlled conditions. By law in Canada, raw milk itself cannot be sold to consumers, but certain raw milk cheeses are allowed if they are made in ways that eliminate harmful bacteria. We strictly follow those rules. 

Aging Raw Cheeses for Safety and Flavor

Our raw cheeses are aged well beyond the minimum 60 days. During this aging, the cheese becomes acidic and loses moisture, creating an environment where pathogens cannot survive long-term. By the time our raw milk pecorino is ready to eat, it has gone through months of fermentation and drying. Tests and industry data show that properly aged raw cheese rarely contains any E. coli, and if it does, it’s at extremely low, safe levels. We also start with exceptionally clean raw milk (thanks to our healthy sheep and hygiene), and we test our batches. In short, we only release raw milk cheese that meets strict safety standards. The result is a traditional cheese with rich flavor complexity and a safety profile we stand behind.

Secondly, we offer raw milk kefir for pets (and some adventurous customers). This might sound unusual, but many pet owners have discovered the probiotic benefits of raw kefir for their cats and dogs. We label it for pet use to stay within regulations, since selling raw milk for human consumption is not allowed. However, the process we use to make kefir addresses safety in a different way: through fermentation. We add authentic kefir grains to fresh raw sheep milk and let them work their magic for 48 hours. The kefir microbes rapidly consume the lactose and acidify the milk. As we noted earlier, this sharp fermentation effectively inhibits harmful bacteria. 

Raw Milk Kefir: Fermentation That Neutralizes Pathogens

By the end of fermentation, what started as raw milk has transformed into a tangy, cultured drink teeming with good bacteria – and essentially no viable E. coli. In fact, research found that raw milk kefir was able to suppress E. coli growth by nearly 5 log units (a 100,000-fold reduction). This means any stray pathogens are virtually wiped out. We still handle it with care and keep everything meticulously clean. We even make our raw milk products on different days to make sure raw and pasteurized products do not come into contact with each other. 

Therefore, we and many of our customers feel confident that our raw kefir is generally accepted as safe due to this natural bio-protection. Our own pets lap it up daily and thrive on it. It’s worth noting that our kefir is made from sheep’s milk, which has its own advantages. 

Sheep Milk Kefir

Sheep milk is naturally an A2-type milk and is rich in proteins and medium-chain fats, often making it gentle on digestion. When fermented, it becomes a highly digestible beverage. We like to call it sheep milk kefir, and it’s one of the unique products of our farm. Our sheep are 100% pasture-raised, so you’re getting truly grass-fed kefir made from the milk of animals that graze on wildflowers and grass. This gives our kefir a distinct, rich taste and a nutritional profile enriched by the grass-fed diet (like higher omega-3s and CLA in the milk fat).

We carry forward the old-world tradition of fermented sheep dairy, and we’re proud to share it with you – transparently and passionately. (Transparency and trust are core to us. Please feel free to watch our behind-the-scenes videos where we show how we handcraft each cheese and ferment each batch of kefir. Better yet, come visit us! You can meet our friendly sheep, see our cheesemaking in action, and enjoy a farm brunch or cheese & charcuterie tasting. We believe seeing is believing when it comes to responsible farming.)

Kefir: Fermentation that Fights Lactose and Bad Bacteria

Kefir is often called a “living” drink – and for good reason. It’s a fermented milk beverage packed with live probiotics. From a farmer’s perspective, kefir fermentation is fascinating because it not only preserves milk but actually improves it in some ways. Two big benefits stand out: kefir bacteria consume lactose (the sugar in milk) and kefir’s probiotic cultures kill or inhibit harmful bacteria. This makes kefir an ally for both gut health and food safety. Let’s break down what happens when we make kefir. 

We introduce kefir “grains” into milk; these grains are colonies of friendly bacteria and yeast. Over about 24 to 48 hours, those microorganisms feast on lactose and convert it into lactic acid, carbon dioxide, and small amounts of alcohol. The lactic acid is what gives kefir its sour taste – similar to yogurt but sharper. For lactose-intolerant individuals, this is excellent news. Much of the lactose is gone, and what remains is paired with lactase enzymes produced by the microbes. In effect, kefir is a nearly lactose-free kefir product. 

Lactose-Free Kefir for Easy Digestion

Studies have shown that fermented dairy, like kefir, is generally well-tolerated by people who cannot drink regular milk. The friendly bacteria pre-digest the lactose for you. This is why some refer to kefir as “the lactose-free milk.” (It’s 99.9% lactose-free; it typically contains only a fraction of the lactose found in milk.) Many of our customers who struggle with milk find that they can enjoy our milk kefir or raw milk kefir cheeses without any trouble. It’s an excellent way to get the calcium and protein from milk without the lactose woes. 

Now onto the second superpower of kefir: its ability to fight bad bacteria. Kefir is teeming with a diverse community of probiotics – by some counts, up to 100+ strains of bacteria and yeasts live in authentic kefir. Among these, a standout is Lactobacillus kefiri, a probiotic bacterium unique to kefir. Research indicates that L. kefiri and other kefir microbes produce antimicrobial substances that can inhibit pathogens like Salmonella and E. coli

Healthline summarizes that kefir has potent antibacterial properties, demonstrating the ability to stop harmful bacteria from growing. In practical terms, when you drink kefir, you are ingesting a squad of “good bugs” that can help keep the “bad bugs” in check, both in the kefir itself and in your digestive system. Think of kefir as a gut health powerhouse (kefir gut health is a popular topic in nutrition circles). The probiotics in kefir travel to your intestines and help bolster the population of beneficial bacteria. This creates a hostile environment for nasty invaders. A balanced gut flora from probiotic foods can crowd out or directly neutralize pathogens. For example, kefir consumption has been linked to fewer gastrointestinal infections and improvements in chronic digestive issues. It’s known to help restore gut balance after antibiotic use and can even relieve certain types of diarrhea. 

A Probiotic Powerhouse Against Harmful Bacteria

All of this aligns with the age-old wisdom: fermented foods are healing foods. Kefir, in particular, is like the champion of fermented dairy. It’s more potent in probiotics than yogurt, owing to the symbiotic yeast and bacteria present. From a safety standpoint, as we discussed earlier, kefir’s acidity and probiotic arsenal make it self-protective. Harmful bacteria such as E. coli cannot multiply in finished kefir. This is analogous to how those same kefir microbes act in your gut. They produce acids (like lactic and acetic acid) and natural antibiotics that inhibit pathogens. 

Drinking kefir is like sending an army of good microbes into your digestive tract to chase away the bad actors. That’s why many pet owners give our kefir to their dogs or cats with digestive problems. And that is why we ourselves drink kefir daily for its gut health benefits. In summary, kefir fermentation transforms milk into a tart, tangy, effervescent beverage that is low in lactose and rich in probiotics. It exemplifies how traditional food processing can enhance safety and nutrition simultaneously. Our sheep kefir (made from sheep’s milk) is an example of using an age-old method to create a modern health drink. It’s safe (even when made with raw milk for pets, as the fermentation safeguards it) and profoundly beneficial. We encourage anyone curious about kefir to give it a try – your gut will thank you!

Empowering Your Own Decisions

Ultimately, this discussion underscores the importance of personal responsibility in health choices. While governments can provide guidelines and ensure basic safety standards, only you can decide what trade-offs you are willing to make for your health and well-being. We encourage every reader to take an active role in understanding and directing their own health journey. Rather than blindly depending on a production company or a government to tell you what is “good” or “bad” for you, arm yourself with knowledge and make thoughtful choices. In practice, this means you should:

Do your own research: Inform yourself by consulting reliable sources, scientific studies, and diverse viewpoints before accepting a health claim or policy at face value.

Ask questions: Be curious and critical. If a specific food processing method or medical recommendation is presented as the only option, ask why—question whether there might be alternatives or hidden downsides.

Make your own informed decisions: After weighing the evidence and considering your personal values, take charge of your choices. What works for someone else – or even what the law permits – might not align with what you believe is best for your body or family.

By being proactive in this way, you retain your freedom while also taking accountability for your health. It is indeed a challenging balance to strike – embracing liberty yet exercising wisdom and caution – but it is also a profoundly empowering one. In the end, no government regulation or industry promise can substitute for your own informed judgment. So, cherish your freedom, use it responsibly, and remember that your health is ultimately in your hands.

Conclusion and Invitation

Protecting our customers from bacteria like E. coli while delivering nutritious dairy is a responsibility we carry with pride. The main source of E. coli is the natural world around us, but through careful farm practices, pasteurization, and fermentation, we keep it out of your milk. The consequences of E. coli infection can be severe, so we never take shortcuts on safety. Modern farms like ours use pasteurization to eliminate pathogens and fermentation to add an extra layer of protection (and to craft delicious foods!). 

At Secret Lands Farm, we have chosen a path that honors tradition with transparency. From our low-temperature pasteurization that preserves milk’s goodness to our raw aged cheeses and lactose-free kefir that showcase the art of fermentation. We want you to know exactly how your food is made and to feel the passion we put into every wheel of cheese and every bottle of kefir.

To Our Community

Thank you for reading this far and learning about our approach. We hope it was easy to understand and gave you valuable insights into dairy safety and kefir fermentation. If you have any more questions or if there’s another related topic you’d like us to explore in an article, please contact us. We’re always happy to share what we know – after all, we believe an informed community is a healthier community. 

And of course, consider this an open invitation to visit our farm for a tour or tasting. Come see our grass-fed sheep up close. Watch how we make our artisan cheeses and kefir, and enjoy the results for yourself. From our farm to your family, we are committed to offering dairy products that are safe, wholesome, and transparently produced. 

Feel free to reach out to Secret Lands Farm for any further information or to schedule a visit. Stay healthy and enjoy the rich tradition of safe, fermented dairy!

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