Antibiotics and the Horse's Digestive Tract

At some point in most horses’ lives, they will get an infection and need a course of antibiotics or antimicrobials. Antibiotics are specific to killing off bacteria, whereas antimicrobials target bacteria plus other microbes, like fungi. For the purposes of this article, we will use the broader term antimicrobial, as both antimicrobials and antibiotics impact equine digestive health similarly.

Just like with us, antimicrobials are meant to support the immune system to help fight off an infection caused by microbes (bacteria, fungus, and others). Generally, many of the first-line antimicrobials prescribed to horses are not very microbe specific, and they will impact the entire body of the horse. This means that antimicrobials will kill off microorganisms indiscriminately, including the beneficial microbes in a horse’s digestive tract.

The Importance of Your Horse’s Gut Microbiome

We have previously published an article on the Importance of Equine Hindgut Microbes. In this article, we highlight just how critical they are to equine nutrition; so much so, that studies to better understand the equine microbiome continue to be a hot topic in nutritional research. We now have direct links with the population and types of microbes in the gut of the horse and their impacts on the overall health of the horse.

There are numerous different microbes in the equine digestive tract. For example, it is estimated that there are at least a population of 1015 bacteria in the horse’s colon, which is over 10 quadrillion individual bacteria. In addition to bacteria, other microbes in the gut of the horse include:

  • Fungi
  • Protozoa
  • Archaea

Many of these different types of microorganisms are critical to digestion. For example, certain microbes in the horse’s gut are critical to the breakdown of the cellular walls of forage, which allows the horse to draw nutrients from it.

Conversely, we know certain types of lesser desirable microbes in the hindgut of the horse can be problematic. For example, certain types of bacteria will feast on high levels of non-structural carbohydrates (NSC) in the hindgut and increase the risk of negative health impacts, such as laminitis and diarrhea.

What Happens When the Horse’s Gut Microbiome Is Upset?

There is a lot that can alter a horse’s gut microbe population. For example, domestic horses, compared to their wild counterparts, have a much different microbiome due to the differences in diets. The next major impact on the gut microbe population is thought to be the impacts of medications, primarily the antimicrobials. Other factors, like stress from transport, exercise, or social interactions, can also alter the balance. Even fasting for over 24 hours can alter the microbial population of a horse’s digestive tract.

If the balance of microbes in the horse’s gut are too out of balance, it can lead to many detrimental health issues, or, in some worst-case circumstances, death. Some of the more concerning health issues include:

  • Colitis, which is inflammation of the gut lining in the hindgut that is common after giving antimicrobials. Colitis can be life threatening.  
  • Laminitis is the imbalance of microbes leading to massive die off of beneficial bacteria that are then absorbed by the horse. This can lead to the inflammation of the laminae tissue in the horse’s hoof.  
  • Colic. Numerous types of colic can be caused by an imbalance of gut microbes.

Emerging research in multiple species are showing even more links to overall health and the population of microbes in the gut. In humans, disturbances in the microbiome have been associated with inflammatory bowel disease, cancers, diabetes, and other disorders. Research of the microbiome in the horse is ongoing and is leading to a greater understanding of equine nutrition and health.

How Antimicrobials Affect the Horse’s Gut Microbe Population

As stated, antimicrobials are not always specific on the microbes they kill off. We know that antimicrobials can lead to gastrointestinal disturbance in the equine microbiota. Studies have shown that after treatment with antimicrobials, horses experience an alteration to the fermentation patterns in the hindgut. One clear sign of this disturbance in the horse is diarrhea after treatment.

Studies have also linked changes in the population of gut microbes based on which antimicrobial was given and how it was administered. For example, TMS (trimethoprim sulfadiazine) has a much harsher impact on the microbe population in the horse’s gut as compared to penicillin. This is because TMS kills off a wider range of microbes compared to the narrower spectrum of penicillin. Also, in the study, TMS was given orally, whereas penicillin was given as an injection. However, it is worth noting that even when injected, antimicrobials can impact the horse’s gut microbes.

Once given, antimicrobials begin to change the gut microbe population almost immediately (within 24 hours of treatment). In the horse, major changes in gut microbe populations are first noticeable after 5 days of treatment. Once treatment has ceased, it is estimated it takes about 25 to 30 days for the gut microbe population to return to baseline.

Supporting Your Horse’s Gut Microbiome After Antimicrobials 

During and after a course of antimicrobials, there are steps horse owners can take to support a healthy gut microbe population. Our article Supporting Your Horse’s Hindgut Health highlights some of these important considerations and they are worth repeating here. These tips include:

  • Ensuring horses have access to plentiful high-quality forage. After treatment with antimicrobials, free choice hay may be wise to help re-establish and support healthy gut microbe populations. 
  • Feeding pre- and probiotics is critical. The prebiotics help feed and support beneficial gut microbes. Probiotics help establish healthy microbes and yeasts in the horse's hindgut. It is often recommended to feed them during and after antimicrobial treatment. 
  • Ensure feeding times are well-spaced out with small meals throughout the day and not more than 5 pounds of horse feed per meal for a 1000-pound horse. 

The primary goal is to support your horse’s gut health, while allowing time for the healthy microbe populations to re-establish themselves.

There are also specialty items, like the Constant Comfort® Total Gut Health System, that are also beneficial in helping horses after treatment with antimicrobials. Constant Comfort® is specially designed to support stomach and overall gut health with focused nutrients and pre- and probiotics. It also helps buffer the horse’s digestive tract, which is often upset after antimicrobial treatment.

All in all, horse owners need to be cautious and monitor their horses during and after treatment of antimicrobials (antibiotics). With a carefully managed feeding plan, horses can transition through treatment just fine. If you have any questions or concerns about your horse during or after treatment with antimicrobials, please feel free to contact us for a free consultation.


Costa, M., et al. (2015). Changes in the equine fecal microbiota associated with the use of systemic antimicrobial drugs. BMC Veterinary Research. 11:19.

Kauter, A., et al. (2019). The gut microbiome of horses: current research on equine enteral microbiota and future perspectives. Animal Microbiome. 1:14.

Article By: Nicole Rambo, Ph.D. & Chris Mortensen, Ph.D.
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