Pet Diarrhea: Why You Should Think Twice Before Giving Antibiotics

April 1, 2024

By Sarah Griffiths, DCH

In recent years, the use of antibiotics in veterinary medicine has come under scrutiny due to their potential long-term effects on pet and human health. Among these antibiotics, metronidazole (also known as Flagyl) has gained attention for its association with disrupting the gut microbiome, leading to adverse consequences that may persist long after its use. Today, we’re exploring the detrimental effects of metronidazole on the gut microbiome and the implications for their overall health, drawing upon research from both veterinary and human medicine.

What is an Antibiotic and What is the Purpose of Using One?

Definition of Antibiotic: An antibiotic is a type of antimicrobial medication used to treat BACTERIAL infections in both humans and animals. Antibiotics work by either killing bacteria or inhibiting their growth, thereby helping the body’s immune system to overcome the infection.

Responsible Uses of Antibiotics in Veterinary Medicine

Antibiotics may be used in many scenarios where the benefits are greater than the risk of negative effects as such as:

  1. Treatment of Bacterial Infections: Antibiotics are essential for treating harmful bacterial infections – as per a bacterial culture performed by your veterinarian –  in animals, including skin infections, respiratory infections, urinary tract infections, and more. Whenever possible, a bacterial culture should be done to determine the best course of action when it comes to infections.
  2. Prevention of Infection: Antibiotics may be used prophylactically to prevent infections in certain situations, such as for invasive internal surgeries.

Irresponsible Use of Antibiotics

Irresponsible use of antibiotics should be taken seriously and can result in more risk than benefit. :

  1. Viral Infections: Antibiotics are ineffective against viral infections, such as canine distemper or feline leukemia. They should not be used as a treatment for viral illnesses.
  2. Non-Bacterial Conditions: Antibiotics should not be used to treat conditions that are not caused by bacterial infections, such as in the instance of immune-mediated inflammation. Using antibiotics inappropriately can contribute to antibiotic resistance and may disrupt the balance of microbial communities in the body and further disrupt immune function.
  3. Growth Promotion in Agriculture: The use of antibiotics as growth promoters in animal agriculture is a controversial practice that has been linked to the development of antibiotic-resistant bacteria. In many regions, the use of antibiotics for growth promotion purposes is being restricted or banned.
  4. Prophylactic Use Without Justification: Prophylactic use of antibiotics in animals without a clear medical indication or risk of infection should be avoided, as it can contribute to antibiotic resistance and the development of superbugs. This is happening at an alarming rate and needs to stop. As a pet parent, please be a part of the solution!

Causes of Diarrhea are Not Always Bacterial in Nature!

Diarrhea in pets has a wide range of causes. Most are not related to bacterial infection.

  1. Dietary Changes: Switching to a new type or brand of food too quickly can upset a pet’s digestive system.
  2. Food Allergies or Intolerances: Some pets may be allergic or intolerant to certain ingredients in their food, leading to gastrointestinal upset.
  3. Ingestion of Foreign Objects: Pets may ingest objects that are indigestible or toxic, causing irritation or blockages in the digestive tract.
  4. Bacterial Infections: Bacteria such as Salmonella or E. coli can cause gastrointestinal infections in pets.
  5. Parasites: Intestinal parasites such as roundworms, hookworms, or giardia can lead to diarrhea in pets.
  6. Viral Infections: Viruses such as parvovirus or coronavirus can cause diarrhea, especially in puppies and kittens.
  7. Stress or Anxiety: Changes in environment, routine, or social dynamics can stress pets and lead to gastrointestinal issues.
  8. Medication Side Effects: Some medications, especially antibiotics, can disrupt the balance of bacteria in the gut and cause diarrhea as a side effect.
  9. Toxic Ingestion: Consuming toxic substances like certain plants, chemicals, or human foods can lead to gastrointestinal upset and diarrhea.
  10. Inflammatory Bowel Disease (IBD): Chronic inflammation of the gastrointestinal tract can cause diarrhea, vomiting, and weight loss in pets.
  11. Pancreatitis: Inflammation of the pancreas can lead to digestive disturbances, including diarrhea.
  12. Endocrine Disorders: Conditions such as hyperthyroidism or Addison’s disease can affect gastrointestinal function and cause diarrhea.
  13. Organ Dysfunction: Diseases affecting organs such as the liver or kidneys can manifest symptoms including diarrhea.
  14. Food Poisoning: Contaminated or spoiled food can cause food poisoning and result in diarrhea.
  15. Heatstroke: In hot weather, pets can suffer from heatstroke, which can lead to diarrhea along with other symptoms like vomiting and lethargy.

You’ll notice that the majority of the above issues are NOT caused by bacteria….

Metronidazole and Gut Microbiome Disruption (Dysbiosis)

Metronidazole, commonly prescribed by veterinarians to treat various gastrointestinal issues including diarrhea in pets, belongs to the class of antibiotics known as nitroimidazoles. While effective in targeting certain bacterial infections, metronidazole does not discriminate between harmful and beneficial bacteria in the gut, leading to a disruption in the delicate balance of the microbiome, known as dysbiosis.

Veterinary research has highlighted the profound impact of metronidazole on the gut microbiota of pets. A study by Jergens et al. (2019) demonstrated that metronidazole treatment in dogs with acute hemorrhagic diarrhea syndrome resulted in significant alterations in the composition and diversity of the gut microbiome, persisting for up to two years post-treatment. Similar findings have been reported in human medicine, emphasizing the universality of this issue.

Unfortunately, acute gastro-intestinal conditions often result in the pet having the kitchen sink thrown at them when it comes to medications. There is often no investigation as to the cause of the diarrhea (eg. through fecal culture testing, blood testing or other diagnostic tools). A knee-jerk prescription could be more detrimental to your pet than you think. Antibiotics often work for a short time with diarrhea returning and becoming a chronic condition over time, even leading to more serious gastro-intestinal issues like irritable bowel disease and even immune-mediated issues such as skin allergies.

Pet parents may find it is in their pet’s best interest to consider customized functional testing and treatments for this common digestive issue…..

My case load includes a large number of animals who have been subjected to multiple rounds of metronidazole for chronic diarrhea only to find that the problem worsens over time and comes back with a vengeance after each prescription of antibiotics. Some of my clients have also experienced even more detrimental side effects including immune-mediated skin and gut disorders after several rounds of antibiotics. Secondary bacterial skin infections (staphylococcus and yeast) are also common in these cases pointing in the direction of not only disruption in the gut microbiome but the skin’s microbiome too.

These cases are difficult to manage, often require intervention with immune-suppressive drugs for quality of life and take a long time to resolve with integrative tools. Can you relate?

World Health Organization’s Antibiotic Warning

In light of the rising concern over antibiotic resistance, the World Health Organization (WHO) has issued a statement urging veterinarians to exercise caution when prescribing antibiotics for minor illnesses in animals. According to WHO, antibiotic-resistant strains of bacteria contribute to approximately 700,000 deaths globally each year, highlighting the urgent need to curtail the indiscriminate use of antibiotics in both human and veterinary medicine.

Limitations of Probiotic Supplementation

Contrary to popular belief, simply administering probiotics after a course of antibiotics does not fully restore the gut microbiome to its original state. While probiotics can introduce beneficial bacteria to the gut, they do not address the complexity of microbial diversity and ecosystem disruption caused by antibiotics. Research suggests that it may take YEARS for the gut microbiome to recover fully from the effects of even one treatment of antibiotics.

A study by Dethlefsen et al. (2008) demonstrated that although probiotic supplementation can enhance the recovery of the gut microbiome following antibiotic treatment, it does not restore the original diversity and composition of the microbiota. This highlights the importance of adopting alternative strategies to mitigate the long-term consequences of antibiotic use in pets.


The use of metronidazole and other antibiotics in veterinary medicine can have profound and lasting effects on your pets’ gut health. By disrupting the delicate balance of the gut microbiome, these medications may predispose animals to a range of health issues, including gastrointestinal disturbances and immune dysregulation. In light of the growing concern over antibiotic resistance, it is imperative to exercise caution when considering a round of antibiotics and to explore alternative treatment options whenever possible.

Furthermore, pet owners should be informed about the potential risks associated with antibiotic use and encouraged to discuss alternative therapies with their veterinarians. Ultimately, by prioritizing the preservation of the gut microbiome, we can safeguard the long-term health and well-being of our beloved animal companions.


Jergens, A. E., Pressel, M., Crandell, J., Morrison, J. A., & Ruaux, C. G. (2019). Fluorescence in situ hybridization confirms marked similarity between ileal mucosa-associated microbiota of dogs with acute hemorrhagic diarrhea syndrome and controls but no significant changes among time points with Metronidazole administration. Veterinary Microbiology, 239, 108443.

Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008). The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biology, 6(11), e280.

World Health Organization. (2019). Antibiotic resistance: Key facts. Retrieved from