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.

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.

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 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.”

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.

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.

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.

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.

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.

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.

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.

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.