Impact of Antibiotics

Impact of Antibiotics

In This Article

When a veterinarian patient arrives with a chronic case of diarrhea, antibiotics are usually the treatment of choice. However, this frequent use of antibiotics raises the question of the long-term impact of antibiotics on the intestinal microbiome.


Antibiotics in the Veterinary Practice

The intestinal microbiome plays a major role in maintaining the overall health of animals. It contributes to immunomodulation, protection from pathogens, and general metabolism, impacting the individual animal’s health and physiology. Other factors such as age, diet, and environmental components can affect the microbiome and influence gastrointestinal health.

In veterinary medicine, practitioners are routinely presented with acute and chronic cases of diarrhea. In chronic cases, food trials using a hydrolyzed protein source are generally initiated, however, it is not uncommon to administer antibiotics to treat an underlying intestinal dysbiosis. Intestinal dysbiosis is defined as alterations in the normal composition of the microbiome. Antibiotics are often used to treat diarrhea to target causative bacterial pathogens, such as Clostridium perfringens and Giardia.

While these drugs can provide resolution to the clinical signs associated with diarrhea, it raises the question of how short and long-term use of antimicrobials affects the intestinal microbiome. It also raises the question of how important bacteria pertinent to microbiome health are impacted by cases of gastroenteritis and colitis. Metronidazole and tylosin are antibiotics commonly prescribed in cases of acute and chronic diarrhea. 

New Clinical Research on Antibiotics and the Microbiome in Pets

In a recently published study, the use of metronidazole and its effects on the microbiome were evaluated. In this study, they also evaluated the use of a hydrolyzed diet with and without metronidazole. The study concluded that the group of dogs who received metronidazole as well as the group who received the hydrolyzed diet and metronidazole had significant alterations to the microbiome composition.

Certain gut bacteria are known to be important to canine intestinal health and were shown to have decreased due to antibiotic usage. This reduction in key bacteria did not fully resolve 4 weeks after the discontinuation of metronidazole. The canines fed the hydrolyzed protein diet alone did not experience any damage to the microbiome. (Pilla, et al. 2020)

A similar study evaluated the impact of the antibiotic tylosin on the intestinal microbiome of healthy dogs. The study concluded that dogs that received tylosin, experienced fecal dysbiosis, which did not consistently resolve after tylosin cessation. They also determined that the bile acid metabolism in the intestinal tract was altered secondary to antibiotic administration. Bile acids play an important role in maintaining the microbiome. (Manchester, et al. 2019) 


An Alternative to Antibiotics

While there are limited studies that examine the long-term use and impact of antibiotics on the intestinal microbiome in canines, there should be some consideration and caution used when prescribing certain antimicrobials to treat diarrhea. Depending on the presenting case, an alternative option to consider would be the usage of probiotics. A study evaluating the effects of the probiotic, Visbiome, on dogs affected with aseptic acute hemorrhagic diarrhea syndrome (ADHS) concluded that the dogs administered probiotics had an “accelerated normalization of the intestinal microbiome”. Both the group-administered probiotics and the control group experienced recovery with symptomatic treatment alone. (Ziese, et al. 2018) The administration of probiotics adds beneficial live bacteria to the animal’s microbiome. These bacteria contribute to maintaining a balanced microbiome, which aids in immunomodulation, protection against pathogens, and proper metabolism of nutrients. High-quality probiotics can be very beneficial for both acute and chronic gastrointestinal conditions and should be considered for use in therapy.



  • Pilla, et al. “ Effects of Metronidazole on the Fecal Microbiome and Metabolome in Healthy Dogs.” Journal of Internal Medicine, vol.34, 2020, pp 1853-66. Wiley Online Library, doi:10.1111/jvim.15871.
  • Manchester, et al. “Long-Term Impact of Tylosin on Fecal Microbiota and Fecal Bile Acids of Healthy Dogs.” Journal of Internal Medicine, vol. 33, 2019, pp 2605-17. PubMed,
  • Ziese, et al. (2018) Effect of probiotic treatment on the clinical course, intestinal microbiome, and toxigenic Clostridium perfringens in dogs with acute hemorrhagic diarrhea. PLoS One 13: e0204691.
Author's Name

Dr. Dana Hogg

Dr. Dana Hogg graduated in 2015 from North Carolina State University. She grew up in Wilson, North Carolina. Growing up with several animals, Dr. Hogg was drawn to the field of veterinary medicine at a young age. She completed her undergraduate degree at NCSU in 2009 and her master's degree in 2011.