Has Your Dog Been Prescribed Metronidazole? Important Information All Owners Should Know

What is metronidazole, and why is it used? Is it safe for my dog? How can I protect my dog’s important gut bacteria while they take metronidazole? We answer these questions and more. Keep reading to learn what the latest scientific research says about metronidazole and how to best discuss its use with your veterinarian.

If your dog has diarrhea, a course of metronidazole (also known by the brand name Flagyl®) might be the appropriate treatment. But for many veterinarians, use of this antibiotic has become a knee-jerk response to dog diarrhea based on historical practice rather than scientific evidence. A growing body of research suggests that metronidazole is much less effective for some gastrointestinal (GI) conditions than was previously thought. And now we know that in addition to causing troubling side effects, metronidazole can cause unhealthy long-term changes in your dog’s gut microbiome.

Because metronidazole works well for certain conditions that cause diarrhea (such as C. diff infections), it’s become the most frequently used antibiotic for dog diarrhea in general. But in many of these cases, metronidazole may be the wrong choice. Several studies have found, for instance, that metronidazole doesn’t actually help inflammatory bowel disease (IBD) or acute diarrhea in dogs, and its use negatively affects good bacteria in the gut.

So is metronidazole the right diarrhea treatment for your dog? Or will it do more harm than good? We’re here to help. Here we discuss some appropriate and inappropriate uses of this drug, provide some current research that contradicts older assumptions, and give you some questions to ask if your veterinarian suggests metronidazole for your dog.

When Is Metronidazole the Right Choice?

Metronidazole is an extremely useful antibiotic and antiprotozoal medication that’s been around since the 1950s. In both human and veterinary medicine, it’s used to treat infections caused by anaerobic bacteria (bacteria that don’t need oxygen to survive). Since it kills the bacteria, rather than simply halting their growth, metronidazole has the potential to work faster and more efficiently than other antibiotics (such as clindamycin) that also target anaerobic bacteria.

Metronidazole is effective against Bacteroides fragilis, for example, which is a normal bacterial member of the gut and mouth microbiomes but can also be a culprit in wound infection, abscesses, chest infection (often associated with pneumonia), and liver infection. Metronidazole is also used to treat infections of the gallbladder and bile ducts, and because it can enter bone, it’s useful for dental infections involving the jaw.

Metronidazole also works well against Clostridioides—a group of bacteria that includes Clostridium difficile (C. diff), which is a well-known cause of diarrhea in humans and animals.

In both cats and dogs, metronidazole may be useful to treat cases of gastritis caused by Helicobacter bacteria (such as H. pylori) in the stomach. It’s also a valuable weapon against sepsis, a life-threatening immune system response that damages tissues and organs. When it’s used for Helicobacter therapy and for sepsis, metronidazole is usually combined with other antibiotics in order to cover a broader range of bacteria.

In the past, metronidazole worked well against Giardia, a protozoan parasite that causes diarrhea in dogs. Over time, however, that organism has developed a resistance to metronidazole, so this medication is no longer effective by itself against Giardia. (We’ll have more to say about the problem of antimicrobial resistance a little later in this article.)

Study Urges Caution in Choosing Metronidazole

Along with the troublemaking bacteria they’re intended to target, most antibiotics also kill off a lot of the “good” bacteria the body needs for healthy digestion and immune system function. As a result of metronidazole treatment, important members of the gut microbiome can go missing, leading to unhealthy bacterial imbalances. A 2020 study published in the Journal of Veterinary Internal Medicine has found just that; it calls attention to the strong effects metronidazole has on the gut microbiomes of dogs.

The study found that in healthy dogs, a 14-day course of treatment with metronidazole resulted in significant changes in the composition of the gut microbiome. Metronidazole treatment was associated with decreases in important beneficial bacteria, such as Fusobacteria—one of the dominant groups of bacteria in the gut microbiomes of dogs (and cats). Treatment was also associated with reductions in overall richness, a term used to measure the health of the microbiome by examining the number of different bacterial species present. And these effects weren’t just temporary: four weeks after the dogs had stopped receiving metronidazole, these microbiome changes still had not fully resolved, meaning that these dogs still didn’t have enough of some of the bacteria necessary for healthy gut function.

The study’s authors recommend that veterinarians adopt a more cautious approach when using metronidazole in dogs, especially in dogs that may already have imbalanced gut microbiomes.

This study gained a lot of attention among pet parents when it was highlighted in a Facebook Live event by integrative veterinarian Dr. Karen Becker and pet wellness educator Rodney Habib. Becker and Habib discussed the potential overuse of metronidazole for cats and dogs with diarrhea, pointed to several alternative treatments for GI issues, and emphasized the importance of testing your pet’s gut health after a course of metronidazole or any other antibiotic.

Inappropriate Uses of Metronidazole: What the Latest Science Suggests

Because past research has found metronidazole to be effective against certain causes of diarrhea in dogs, it became many veterinarians’ go-to treatment for diarrhea in general. The problem is that there isn’t much scientific evidence that metronidazole actually helps some of the conditions it’s being used for. And yet, even without strong scientific evidence of its effectiveness, metronidazole has become the most commonly prescribed antimicrobial medication for acute diarrhea in dogs. Here are common situations in which research has found metronidazole not to be the best choice:

Giardia Infection

In the past, metronidazole was commonly used to treat infections caused by the parasites Giardia and Tritrichomonas, which are known to cause diarrhea in both cats and dogs. Over time, however, both of these organisms have developed metronidazole resistance, so that metronidazole by itself is no longer a sufficient treatment for these protozoal infections.

E. coli Infection

An overgrowth of Escherichia coli (E. coli) bacteria in the gut is a very common cause of diarrhea in dogs. According to AnimalBiome’s own data, 1 in 3 dogs have too much E. coli in their gut microbiome. Metronidazole is the most common antibiotic prescribed for dogs with diarrhea caused by an E. coli overgrowth, but 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.

Inflammatory Bowel Disease (IBD)

Because metronidazole has a positive effect on Crohn’s disease in humans, it is often used for diarrhea in dogs with IBD and other chronic diseases of the intestines, usually in combination with the steroid prednisone. However, researchers established in 2010 that metronidazole doesn’t actually add any benefit in this scenario: prednisone plus metronidazole is no more effective for IBD than prednisone by itself.

Acute Diarrhea

Acute diarrhea is defined as three or more loose or watery stools in a single day. It can be stressful when your dog develops a case of acute diarrhea and the cause is unknown.

Because of its historical effectiveness against such diarrhea-inducing agents as Giardia and C. diff, metronidazole has been increasingly used by veterinarians to manage diarrhea due to other causes. But there is little evidence that it actually helps acute nonspecific diarrhea (diarrhea with an undetermined cause)—a category that represents most diarrhea cases in both cats and dogs.

In the veterinary world, there is some evidence that metronidazole reduces the time it takes for acute diarrhea to resolve. However, researchers at the University of Michigan found in their study that this reduction amounted to only a couple of days in dogs. And as the authors pointed out, most cases of diarrhea in dogs resolve in a few days “regardless of treatment.”

Published in Frontiers in Veterinary Science, another study that looked at treating acute diarrhea in dogs found no significant difference between metronidazole and a placebo. The authors concluded that the use of metronidazole for dogs with acute diarrhea “should be discouraged until evidence-based data demonstrate a difference in treatment outcome.”

Questions to Ask If Your Veterinarian Prescribes Metronidazole

While metronidazole has been shown to be an appropriate choice for some conditions, in other cases, it may not be as effective as many veterinarians assume. And sometimes veterinarians prescribe antibiotics because they think the pet parent wants them. We recommend that you talk with your veterinarian about whether metronidazole will be beneficial for your dog and whether there are any other options to consider. Here are some questions to ask:

Does My Dog Need Antibiotics?

In many cases of dog diarrhea, the answer may be no. Though some health issues, such as life-threatening bacterial infections, do require antibiotics, other conditions may resolve with supportive care alone. Supportive care includes a bland diet, rest, and access to unlimited fresh drinking water.

For example, dogs with bloody diarrhea (hemorrhagic gastroenteritis) are often given antibiotics, but according to veterinary consensus guidelines, antibiotics are appropriate for this condition only when sepsis is present. Researchers have found that as long as sepsis is not involved, even hemorrhagic gastroenteritis responds just as well to supportive care as to antibiotics.

In fact, several studies have shown that metronidazole can actually make diarrhea worse, not only by reducing populations of “good” anaerobic bacteria, but also by altering the intestinal mucus, which helps to protect your dog's GI tract from inflammation and infection.

What Are the Possible Side Effects of Metronidazole?

Most medications have the potential to cause side effects, so it’s important to ask your veterinarian what to watch out for. Metronidazole has a very bitter taste and often causes excessive salivation, drooling, gagging, or frothing at the mouth, especially in cats. In both cats and dogs, the bitter taste may also cause nausea and loss of appetite (anorexia), so pets taking metronidazole may eat less than usual or refuse meals altogether. Vomiting and diarrhea are also relatively common side effects of this drug.

Less common but more serious side effects of metronidazole in pets include lethargy, weakness, liver damage, and central nervous system disorders. Clinical signs of nervous system toxicity may include abnormal eye movements, head tilt, loss of balance and coordination, stumbling or knuckling, and even seizures. High doses and/or long-term use of metronidazole can have adverse effects as well.  

Some cases of birth defects have been recorded when a dog takes metronidazole tablets while pregnant. Rare reactions in dogs have included dangerously low blood counts. In cats, metronidazole has been found to cause DNA damage to lymphocytes (white blood cells), an important element of the immune system.

Does My Dog Have Any Conditions That Would Make a Bad Reaction to Metronidazole More Likely?

Metronidazole should not be used if your dog has ever had an allergic reaction (such as hives) or other adverse response to this medication in the past. Don’t use metronidazole if your dog might be pregnant. If your dog has liver disease, metronidazole should be used very cautiously and at a low dose. It should also be used cautiously in any animal with a compromised nervous system.

Are There Any Supplements I Can Combine with Metronidazole to Improve the Outcome for My Dog?

Certain pre-, pro-, and postbiotics may help support better outcomes and reduce potential side effects. In a study of shelter dogs with diarrhea, a combination of probiotics and metronidazole led to better overall results than metronidazole alone. When silymarin (an anti-inflammatory flavonoid derived from milk thistle seed) was combined with metronidazole in another study, dogs had better appetite, less intermittent vomiting, and less weight loss than when receiving metronidazole alone.

If you and your veterinarian determine that a course of metronidazole or another antibiotic is warranted in your dog’s case, there’s still a lot you can do to help your dog feel better during and after treatment.

Many antibiotics cause diarrhea as a side effect, but adding the yeast Saccharomyces boulardii to your pet’s food can reduce the risk of antibiotic-caused diarrhea. S. boulardii is a probiotic that works by supporting beneficial gut bacteria and inhibiting the growth of pathogenic (disease-causing) bacteria. AnimalBiome’s Gut Maintenance Plus (GMP), which was specifically designed to help resolve antibiotic-caused diarrhea in cats and dogs, contains S. boulardii in addition to the prebiotics fructooligosaccharide (FOS) and PreforPro®.

And if you and your veterinarian do decide on metronidazole, putting the medication in an empty food-grade capsule (either gelatin or plant-based) will protect your dog from the drug’s bitter taste and reduce the risk of nausea.

What Are the Alternatives to Metronidazole?

Ask your veterinarian whether medications that treat specific aspects of your dog’s GI condition would be appropriate alternatives to an antibiotic. Such symptomatic treatments include anti-nausea medications, proton pump inhibitors or antihistamines like cimetidine to reduce acid production, motility inhibitors (to reduce cramping and the sense of urgency), bile acid sequestrants (to prevent bile acids from being reabsorbed by the body), and vitamin B12 (cobalamin, which may be useful in cases of chronic diarrhea). Some of these approaches may also cause changes to your dog’s gut microbiome, but those changes would likely be much less radical than the effects associated with metronidazole.

Since diarrhea often indicates a disruption in the balance of your dog’s gut bacteria, the prebiotic fibers inulin and psyllium may help by feeding those healthy bacterial populations while also firming up the stool. S. boulardii is another supplement that can help resolve gut imbalances by supporting healthy bacteria. If your dog’s microbiome is significantly out of balance, AnimalBiome’s DoggyBiome Gut Restore Supplement can help by seeding the gut with a whole community of healthy dog-specific bacteria.

A recent study conducted by the Ohio State University College of Veterinary Medicine and published in the Journal of the American Veterinary Medical Association found that diarrhea flare-ups are better managed with an easily digestible diet, with or without psyllium, compared to using metronidazole.

Test Your Dog’s Gut Health after a Course of Antibiotics

After finishing a course of antibiotics, including metronidazole, it’s important to find out what changes the medication might have made to your dog’s unique microbiome. It is especially important to find out whether your dog has a bacterial imbalance (dysbiosis), because the earlier it is resolved, the less long-term damage it can cause.

Testing your dog’s gut health will give you valuable information about which bacterial populations are present, which beneficial strains might be missing, and what specific steps you can take to support your dog’s health. A DoggyBiome Gut Health Test includes a detailed report on all the bacteria that make up your dog’s gut microbiome, as well as personalized diet, lifestyle, and supplement recommendations.

For example, if your dog’s fecal sample shows a deficiency in the important Fusobacteria group of bacteria (which metronidazole is known to significantly reduce), increasing the amount of protein in your dog’s diet may help, since Fusobacteria do best in protein-rich environments. Our DoggyBiome Gut Restore Supplement can replenish beneficial bacteria in your dog’s gut that may have been eliminated during antibiotic treatment.

AnimalBiome’s Perspective

Antimicrobial therapies, including antibiotics, have had a profound impact on both human and animal health. Prior to Alexander Fleming’s discovery in 1928 that penicillin inhibited the growth of bacteria, no treatments existed for infections such as pneumonia, gonorrhea, and rheumatic fever. Many surgical procedures and chemotherapies that are common today would not be possible without the availability of antimicrobial therapies.

Antimicrobial Stewardship

However, as Fleming himself warned, the overuse of antimicrobials can lead to the development of antimicrobial resistance, not only in the bacterial pathogens being targeted but also in other, related microorganisms. The modern world continues to see valuable, life-saving antibiotics lose their effectiveness as dangerous bacteria become resistant to them.

In order to prevent antibiotic resistance, doctors and veterinarians must use these powerful medications judiciously—which includes identifying the actual cause of a given infection through diagnostics and making sure the antibiotic being prescribed has been proven effective against that cause. This approach, known as antimicrobial stewardship, can produce better patient outcomes, reduce resistance to antimicrobial drugs, and decrease the spread of deadly infections caused by multidrug-resistant microorganisms.

Microbiome Disruption

Another danger is the tendency of antimicrobials to disrupt the gut microbiome by causing imbalances (dysbiosis) among the resident bacterial populations. More specifically, there is growing concern regarding the use of antimicrobials in animals whose gut microbiomes are already imbalanced, such as dogs with IBD and other chronic conditions of the gastrointestinal tract.

Given these risks, it’s important to explore any viable alternatives to the use of antibiotics. For example, both probiotics and fecal microbiota transplantation (FMT) have been investigated as alternative approaches to treating IBD and other causes of diarrhea in dogs. A 2020 study published in Frontiers in Veterinary Science concluded that FMT works better than metronidazole in dogs with acute diarrhea because FMT helps to restore gut health, whereas metronidazole “has a negative impact” on the microbiome.

Our Recommendations

We encourage pet owners and veterinarians to discuss these issues. Metronidazole and other antibiotics can be valuable tools, but it’s important to make sure the use of a medication in a given situation is supported by scientific evidence. And if your dog already suffers from an imbalanced gut microbiome, due to chronic GI issues or other health problems, antibiotics should be used only if absolutely necessary.

We also strongly recommend testing your dog’s gut microbiome after a course of any antibiotic. Identifying and correcting any negative changes the medication might have caused in the bacterial community of the gut can make an enormous difference in your dog’s overall health and quality of life.

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