C. difficile in Dogs: A Solution That Works Better Than Antibiotics


Diarrhea is an extremely common occurrence in dogs. But did you know that many cases of diarrhea are caused by a bacterial pathogen called Clostridioides difficile (also known as C. difficile, or C. diff for short)? If you take your sick dog to the veterinarian for frequent diarrhea, your vet will typically run a test on their stool that looks for the presence of particular bacterial pathogens, including Clostridioides difficile. If C. diff is detected in your dog’s stool, it’s very likely the culprit causing their diarrhea.

How C. difficile Affects the Intestinal Tract

Frequent diarrhea isn’t the only problem this pathogen causes. Clostridioides difficile releases inflammatory toxins that actually damage your dog’s digestive tract. In addition, each C. difficile cell has tiny, whiplike tails (called flagella): as the C. difficile cell travels along your dog’s intestinal tract, these tails whip around and create innumerable tiny wounds in the lining of your dog’s gut.

Because a C. diff infection involves a very large number of these bacterial cells, all these tiny wounds add up and can cause severe, lasting damage to your dog’s digestive health.

The Usual Treatment Is Antibiotics

Since C. diff cells can be very damaging, eliminating the pathogen from your dog’s body becomes a top priority. Unfortunately, this can be a rather difficult task. In many veterinary practices, the most common method for treating a C. diff infection is with antibiotics. Usually the course of antibiotics will last one to two weeks.

In many cases, by the end of the antibiotic sequence, the C. difficile pathogen has been eliminated, and the diarrhea has resolved. However, your dog may not be in the clear just yet. Typically, about 20% of patients that contract Clostridioides difficile will have a recurrence of the infection, usually within just 1–2 months.

C. difficile and Recurrent Infection in Dogs

Research suggests that treating C. diff with antibiotics can eliminate the pathogen in the short term—for as long as the antibiotics are present in the system. However, antibiotics also harm the beneficial gut bacteria needed to keep pathogens like C. diff in check. So as soon as the antibiotics are gone, your dog’s imbalanced gut microbiome may provide a perfect breeding ground for more C. diff. By killing off so many beneficial bacteria, antibiotics (like metronidazole) disrupt the gut microbiome and leave it even more vulnerable to another C. diff infection.

To make matters worse, the C. difficile strains can become more resistant to antibiotics with each recurring infection. An increasingly resilient pathogen paired with an increasingly sick dog can create a life-threatening situation.

Treating C. difficile with Fecal Transplant

Because C. diff is growing increasingly common (in both humans and animals), particularly among immunocompromised individuals and in hospital settings, researchers are motivated to find a more effective treatment that doesn’t leave the patient vulnerable to future infections. At the same time, a number of C. diff strains are becoming resistant to common antibiotics, making treatment even more difficult. Numerous studies in humans have demonstrated that fecal microbiota transplant (FMT) offers an effective solution.

Fecal microbiota transplant involves taking stool (containing beneficial bacteria) from a healthy individual and transplanting it—usually via enema or an oral capsule—into the gut of a sick individual. In human studies, FMT has been shown to prevent recurrence in over 85% of C. diff cases, compared to antibiotics’ success rate of 40% to 50%.

Often an imbalanced microbiome is missing key bacteria for healthy gut function. Rather than eliminating all of the C. diff bacteria in the gut (the antibiotic approach), FMT “plants the seeds” of a healthy, diverse microbiome containing bacteria that are able to outcompete C. diff. In addition to fighting pathogens, a balanced gut microbiome provides the foundation for long-term gut health and a strong immune system.

Natural Treatments for C. diff in Dogs

It can be heartbreaking to see your dog suffer from recurrent C. diff infections. One way to help your dog’s gut microbiome resist pathogens like C. diff is by supplementing their diet with S. boulardii, a special probiotic yeast with anti-inflammatory properties. S. boulardii has been shown to safely prevent and reduce diarrhea from multiple causes. And it’s especially helpful for regrowing gut microorganism populations that have been damaged by an infection or a course of antibiotics.

And if your dog suffers from a C. diff infection that keeps coming back, our science-backed Gut Restore Supplement (fecal transplant via oral capsules) can introduce all the healthy bacteria your dog needs to kick C. diff for good.

Learn More

Dog Diarrhea: What You Need to Know

How to Support Your Pet During and After Antibiotics

Shop DoggyBiome

This article was originally published on December 12, 2018, and updated on December 5, 2021, and November 13, 2023.

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C. difficile in Dogs: A Solution That Works Better Than Antibiotics


Table of Contents

Diarrhea is an extremely common occurrence in dogs. But did you know that many cases of diarrhea are caused by a bacterial pathogen called Clostridioides difficile (also known as C. difficile, or C. diff for short)? If you take your sick dog to the veterinarian for frequent diarrhea, your vet will typically run a test on their stool that looks for the presence of particular bacterial pathogens, including Clostridioides difficile. If C. diff is detected in your dog’s stool, it’s very likely the culprit causing their diarrhea.

How C. difficile Affects the Intestinal Tract

Frequent diarrhea isn’t the only problem this pathogen causes. Clostridioides difficile releases inflammatory toxins that actually damage your dog’s digestive tract. In addition, each C. difficile cell has tiny, whiplike tails (called flagella): as the C. difficile cell travels along your dog’s intestinal tract, these tails whip around and create innumerable tiny wounds in the lining of your dog’s gut.

Because a C. diff infection involves a very large number of these bacterial cells, all these tiny wounds add up and can cause severe, lasting damage to your dog’s digestive health.

The Usual Treatment Is Antibiotics

Since C. diff cells can be very damaging, eliminating the pathogen from your dog’s body becomes a top priority. Unfortunately, this can be a rather difficult task. In many veterinary practices, the most common method for treating a C. diff infection is with antibiotics. Usually the course of antibiotics will last one to two weeks.

In many cases, by the end of the antibiotic sequence, the C. difficile pathogen has been eliminated, and the diarrhea has resolved. However, your dog may not be in the clear just yet. Typically, about 20% of patients that contract Clostridioides difficile will have a recurrence of the infection, usually within just 1–2 months.

C. difficile and Recurrent Infection in Dogs

Research suggests that treating C. diff with antibiotics can eliminate the pathogen in the short term—for as long as the antibiotics are present in the system. However, antibiotics also harm the beneficial gut bacteria needed to keep pathogens like C. diff in check. So as soon as the antibiotics are gone, your dog’s imbalanced gut microbiome may provide a perfect breeding ground for more C. diff. By killing off so many beneficial bacteria, antibiotics (like metronidazole) disrupt the gut microbiome and leave it even more vulnerable to another C. diff infection.

To make matters worse, the C. difficile strains can become more resistant to antibiotics with each recurring infection. An increasingly resilient pathogen paired with an increasingly sick dog can create a life-threatening situation.

Treating C. difficile with Fecal Transplant

Because C. diff is growing increasingly common (in both humans and animals), particularly among immunocompromised individuals and in hospital settings, researchers are motivated to find a more effective treatment that doesn’t leave the patient vulnerable to future infections. At the same time, a number of C. diff strains are becoming resistant to common antibiotics, making treatment even more difficult. Numerous studies in humans have demonstrated that fecal microbiota transplant (FMT) offers an effective solution.

Fecal microbiota transplant involves taking stool (containing beneficial bacteria) from a healthy individual and transplanting it—usually via enema or an oral capsule—into the gut of a sick individual. In human studies, FMT has been shown to prevent recurrence in over 85% of C. diff cases, compared to antibiotics’ success rate of 40% to 50%.

Often an imbalanced microbiome is missing key bacteria for healthy gut function. Rather than eliminating all of the C. diff bacteria in the gut (the antibiotic approach), FMT “plants the seeds” of a healthy, diverse microbiome containing bacteria that are able to outcompete C. diff. In addition to fighting pathogens, a balanced gut microbiome provides the foundation for long-term gut health and a strong immune system.

Natural Treatments for C. diff in Dogs

It can be heartbreaking to see your dog suffer from recurrent C. diff infections. One way to help your dog’s gut microbiome resist pathogens like C. diff is by supplementing their diet with S. boulardii, a special probiotic yeast with anti-inflammatory properties. S. boulardii has been shown to safely prevent and reduce diarrhea from multiple causes. And it’s especially helpful for regrowing gut microorganism populations that have been damaged by an infection or a course of antibiotics.

And if your dog suffers from a C. diff infection that keeps coming back, our science-backed Gut Restore Supplement (fecal transplant via oral capsules) can introduce all the healthy bacteria your dog needs to kick C. diff for good.

Learn More

Dog Diarrhea: What You Need to Know

How to Support Your Pet During and After Antibiotics

Shop DoggyBiome

This article was originally published on December 12, 2018, and updated on December 5, 2021, and November 13, 2023.

Suggested Products


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