When it shows up in the news, E. coli sounds like a pretty bad guy. And it’s true that a few specific types of E. coli can make you or your dog sick. But most strains are harmless. In fact, most E. coli bacteria are beneficial members of a healthy gut microbiome, where they typically live in small numbers. 

If the E. coli population in a dog’s gut grows too large, it can crowd out other important bacteria, throwing the microbiome out of balance and causing symptoms like diarrhea and vomiting. And it turns out that 1 in 3 dogs have too much E. coli in their gut. Keep reading to learn more about E. coli and how you can protect your dog from unhealthy levels of this kind of bacteria.

Escherichia coli (E. coli for short) refers to a large group of bacteria that includes many different strains or types. These bacteria commonly live in the intestines of mammals, including humans and companion animals like dogs, where they are normal members of the gut microbiome. 

Most E. coli strains are harmless, but a few particular strains—such as Shiga toxin–producing E. coli (STEC)—are pathogens that can cause severe illness in both animals and people. Depending on the strain involved, an E. coli infection (colibacillosis) can cause diarrhea, vomiting, urinary tract infections (UTIs), stomach pain, fever, respiratory illness, and even blood poisoning (septicemia). Every year, many commercial dog foods and treats are recalled because of contamination with one or more of these harmful strains of E. coli.

Dogs are much less likely than humans to be infected by one of these disease-causing strains. However, an overgrowth of resident E. coli bacteria in the gut microbiome of dogs turns out to be very common. Too much E. coli in a dog’s gut poses a serious threat to their health.

The presence of small numbers of E. coli in a healthy dog’s gut microbiome is normal. Like the thousands of other kinds of bacteria in the gut, they help with digestion, nutrient absorption, and other healthy functions. But when the E. coli population grows too large, it can cause symptoms like diarrhea and vomiting. And when left untreated, an overgrowth of E. coli also increases a dog’s risk of developing a number of other health problems, including immune system reactions and diabetes.

Over the past seven years, AnimalBiome has analyzed tens of thousands of dog poop samples to better understand bacteria’s role in pet health. In looking closely at all that data (check it out for yourself!), we found something totally unexpected: 1 in 3 of those dogs had elevated (unhealthy) levels of E. coli in their gut microbiomes!

While the presence of E. coli was expected, the prevalence of high levels of E. coli—even in dogs who weren’t exhibiting any symptoms—was shocking. Our data show that E. coli overgrowth is one of the most common gut microbiome imbalances in dogs.

Many factors can lead to an overgrowth of E. coli in a dog’s gut microbiome. Here are some of the most common:

• Inadequate transfer of microbes at birth from the mother’s “first milk,” or colostrum
• Poor diet. Some important gut bacteria can’t thrive because they don’t get enough of the nutrients they need.
• Inflammatory disease. E. coli feed on the dead cells and mucus produced by inflammation of the gut lining.
• Exposure to antibiotics. Antibiotics can negatively impact the gut microbiome by killing both harmful and beneficial bacteria.
• Compromised immune system or other underlying health problems
• Environmental issues like contaminated food (common in raw diets) or water

Our data indicate that 4 out of 10 pets have been exposed in the past year to multiple risk factors that could lead to an unbalanced gut microbiome.

E. coli Takes Advantage of Imbalance

Large, troublemaking populations of E. coli generally start out as small, relatively harmless populations. In healthy dogs, the gut microbiome is diverse and sturdy enough to keep the numbers of E. coli appropriate and manageable. But when a dog develops a gut microbiome imbalance—for example, due to one or more of the factors listed above—it becomes more difficult for the rest of the gut’s microbial community to keep the E. coli population small. And given the opportunity, the E. coli population can grow way out of proportion.

In effect, E. coli infections of the lower intestine can snowball. Dogs with elevated E. coli levels are consistently found to have lower gut bacterial diversity. And as that reduced diversity leads to greater imbalance, the E. coli population grows even larger, further lowering diversity, and so on. Additionally, an E. coli infection causes inflammation in the gut lining, triggering an increase in mucus production. Because E. coli feed off the mucus and other byproducts of this inflammation, their population continues to thrive, causing more inflammation and furthering the snowball effect.

Antibiotics Can Make an E. coli Overgrowth Worse

A few specific antibiotics can kill E. coli, but most don’t. After treatment with most antibiotics, E. coli can really thrive in the gut, because many of the beneficial bacteria have been wiped out by the medication, leaving more space and resources for the E. coli to use to multiply. (The use of inappropriate antibiotics to treat a bacterial infection also increases the risk of antimicrobial resistance.)

Even worse, the most common antibiotic prescribed for dogs with diarrhea caused by an E. coli overgrowth is metronidazole (also known by the brand name Flagyl®). And studies have shown that metronidazole is not effective against E. coli. In fact, this study found a significant association between the use of metronidazole and a greater abundance of E. coli in dogs. According to our own data, dogs with high levels of E. coli are more likely to have been taking antibiotics recently than dogs with normal amounts of E. coli.

When we saw how many of the dogs in our gut microbiome database had high levels of E. coli, we decided to investigate further. It turns out there are some amazing reasons for E. coli’s success.

Intestinal inflammation causes damage to the mucosal epithelium (the gut lining). That damage means that more of the cells that make up the gut lining die and are shed. Those dead gut lining cells contain phospholipids and other compounds that are E. coli’s favorite foods. With their food supply increased by inflammation, E. coli can multiply, gaining an advantage in numbers over the healthy microbial populations in the gut.

So dogs with intestinal inflammation—caused, for example, by a high-carbohydrate diet or by a condition like inflammatory bowel disease (IBD)—are much more likely to have elevated levels of E. coli in their gut microbiomes.

Some E. coli strains can produce antibacterial substances that kill friendly neighboring bacteria. By killing off other, beneficial groups of gut bacteria, E. coli takes out the competition and gains more resources for itself. Killing off its neighbors helps E. coli thrive and multiply.

All cells have ways of taking in the nutrients they need to function. E. coli produces a compound called enterobactin that allows it to collect and absorb excess iron from its environment. That iron helps E. coli to grow, but it also makes it more difficult for the immune system’s antibodies to kill these bacteria. So E. coli thrives partly by making it more difficult for a dog’s own immune system to do its job.

The first step toward achieving a balanced, diverse gut microbiome is to know the state of your dog’s gut health. Our easy, at-home DoggyBiome Gut Health Test can give you the information you need to identify and address imbalances early. By making the diet and lifestyle adjustments recommended in your dog’s personalized Gut Health Test report, you can improve or even prevent health problems like inflammatory bowel disease (IBD), diabetes, and obesity.

If your dog’s Gut Health Test report indicates elevated levels of E. coli, then restoring balance to their gut microbiome—and relieving their diarrhea or other symptoms—will require reducing the size of that overgrown population. Once your dog’s E. coli numbers have been brought down to a healthy level, all the other kinds of bacteria your dog needs will have room to grow again, restoring balance to the gut community.

So if E. coli is such a formidable opponent, how do you reduce its numbers?

When dogs have diarrhea or other gastrointestinal issues, the two treatments most commonly prescribed are probiotic supplements and the antibiotic metronidazole. But neither of these treatments is actually effective at reducing elevated levels of E. coli.

Probiotics cannot directly address an overgrowth of any particular kind of bacteria. Usually, they add small numbers of non-native bacteria that do not impact E. coli levels. And while the antibiotic metronidazole kills a range of different bacteria, it does not kill E. coli. In fact, by thinning out the healthy bacterial groups that we want to support, metronidazole can actually make it easier for the E. coli population to expand.

One special probiotic that does help is S. boulardii, which is a species of yeast rather than a kind of bacteria. Researchers at the University of Bologna found in their study that supplementation with S. boulardii significantly improved the symptoms of chronic diseases of the dog intestinal tract (like E. coli infection), leading to better stool consistency and improved overall body condition.

To combat unhealthy levels of E. coli in the gut, bacteriophages (phages) have proven much more effective than either bacterial probiotics or antibiotics like metronidazole. Bacteriophages (the name means “bacteria eaters”) are naturally occurring organisms that target and kill specific kinds of bacteria.

PreforPro® is a patented mixture of phages that has been clinically proven to reduce unhealthy levels of E. coli in the gut. We use PreforPro in our DoggyBiome GMP supplement, which is specifically designed to reduce diarrhea caused by an overgrowth of E. coli. GMP also contains prebiotics to feed the gut’s beneficial bacteria, helping those populations recover and restoring balance to the microbiome.

As mentioned above, the yeast S. boulardii has been scientifically proven to improve symptoms of chronic gastrointestinal tract diseases in dogs. Our DoggyBiome S. boulardii + FOS Powder effectively introduces this important probiotic to your dog’s intestinal tract along with beneficial prebiotics. The powder can be used in combination with the DoggyBiome GMP supplement to target an E. coli problem from multiple angles.

For dogs whose Gut Health Tests show high levels of E. coli, we often recommend our DoggyBiome Gut Cleanse Powder. This supplement also uses PreforPro to specifically target and kill E. coli.

A balanced, diverse gut microbiome is crucial for almost every aspect of your dog’s well-being. Good gut health is essential not just for digestion and nutrient absorption, but also for the proper functioning of your dog’s immune system (70%–80% of the body’s immune cells live in the gut). Your dog’s skin, coat, brain functions, and mood are also influenced by the gut microbiome.

And if the thousands of different bacterial groups in your dog’s gut aren’t present in the right proportions, some of the microbiome’s important functions stop working properly. Uncomfortable symptoms like diarrhea, vomiting, and scratching can be signs that your dog’s gut microbiome is out of balance.

Early detection of a bacterial imbalance or other gut health issue can help prevent problems down the road. That’s why regular gut health testing is important, even for apparently healthy dogs.

Learn more about our DoggyBiome Gut Health Test.

Newborn puppies and very young dogs are especially vulnerable to E. coli because their immune systems are not fully developed. (Senior dogs and dogs with compromised immune systems are also more susceptible.)

Symptoms of E. coli infection in puppies tend to appear suddenly and can quickly become life-threatening. See a veterinarian immediately if your puppy has any of these clinical signs:

• depression
• lethargy
• weakness
• diarrhea
• vomiting
• lack of appetite
• dehydration
• rapid heart rate
• low body temperature
• bluish mucous membranes (gums, lips, nostrils, ears, anus)

Immediate care is especially important for puppies and dogs who are not fully vaccinated against canine parvovirus, because E. coli infection can make parvo more severe.

A veterinarian will usually take blood, urine, and/or fecal samples to check for the presence of E. coli bacteria. A blood sample analysis will also include white and red blood cell counts, which can indicate the presence of bacterial infection.

E. coli infections in humans are usually caused by eating or drinking something contaminated with one of the harmful strains of E. coli bacteria. But that transmission method is much less common in dogs. Despite the numerous recalls of dog food and dog treats found to be contaminated with E. coli (usually during the manufacturing process), dogs typically don’t acquire an overgrowth of E. coli in the gut from ingesting contaminated food or water. Most cases of E. coli infection in dogs are the result of a small, harmless E. coli population growing out of control.

However, for the sake of your dog’s health (and your own), you should still do your best to avoid contact with E. coli in the environment.

Here are some tips to keep you and your dog healthy:

• Don’t let your dog eat poop.
• Don’t let your dog drink from potentially contaminated water sources (toilets, rivers, streets).
• Don’t let your dog eat or drink near animal waste.
• Wash your hands thoroughly if you have any contact with animal feces.
• Always practice safe food handling (with your own food and your dog’s).
• Wash your dog’s food bowl after every meal.
• Wash any human foods (such as vegetables) before feeding them to your dog.
• Wash your hands after handling your dog’s food.
• Pay attention to FDA recalls of animal products.
• Keep your dog away from sick animals and humans. In rare cases, E. coli infections can spread between people and pets. 
• Avoid giving your dog antibiotics unless absolutely necessary.
• Test your dog’s gut health annually (or anytime your dog has symptoms).