The Importance of Equine Prebiotics and Probiotics for Gut Health

Dr. Justin High of Reata Hospital in Weatherford, TX, and Michael Eggleston, Key Account Manager at Kemin Equine, discuss the importance of equine prebiotics and probiotics for gut health.

Question 1. What are prebiotics versus probiotics?

Dr. High:

For us to understand the significance of using probiotics in our horses, we should have a handle on what makes them most effective. For our probiotic cultures to be clinically effective in the wide range of real-world settings we employ them for, they need certain substrates to do their best work. These specific substrates are called prebiotics. 

A prebiotic is one of the keys to successfully employing probiotics in your horse’s health. Basically, these are food sources for the beneficial bacteria we are supplementing to get our clinical effect. Prebiotics are different types of carbohydrates that are typically indigestible within the microenvironment of the equine gut. These carbs, mostly fiber, are the fuels that good bacteria use. When we are looking to increase the quantity of good bacteria within the gut to repopulate or help offset the imbalance of pathogenic bacteria that have overgrown from numerous causes, we need both prebiotics and probiotics.


In contrast to prebiotics, probiotics are live organisms, usually strains of beneficial bacteria or “good bugs.” When it comes to probiotics, there are really two main benefits:

  1. Maintaining the microbial balance in the gut. The probiotic helps maintain a diverse population of microbes in the gut. Increased levels of diversity have been shown to be beneficial to your horse.
  2. Reduction in the number of pathogenic or “bad bugs” in the gut. If harmful microbes begin to multiply, they can crowd out the beneficial bugs and damage the gut lining — sometimes leading to Leaky Gut Syndrome.

Not all probiotics are the same, so it’s important to understand why the probiotic is being fed and what benefit it provides.

Question 2. Why and when should you feed a probiotic? What are some scenarios where horses could especially benefit?

Dr. High:

From a veterinary standpoint, I think of probiotics in two basic applications — I am either trying to treat disease or prevent disease. In a world where the vast majority of the immune system’s competency is centered in the gut, there are few medications or management practices where we can have such an impact on our horse’s health. In terms of treating disease, there are about as many causes of bacterial imbalance as there are different types of bacteria. For that matter, the use of probiotics is one of the only “medications,” if you want to call them that, we will use on horses with great efficacy from birth to old age. Gut health never takes a day off in your horse’s life. So, in my opinion there should not be a question of why to use them, it is when to use them.   

In terms of prevention, the single most reason I can think of is stress. Stress comes in endless varieties in our lives and in our horses. For better or worse, we are oftentimes the number one cause of stress in our horse’s life. Pressure from performance expectations and training are first in line. Add to that the inconsistencies that accompany the rigors of hauling, feeding at odd times of the day or night, and environmental stressors we cannot necessarily control, and you have quite the formula for stress. 

I would say, as a whole, horses are a lot like people in that they tend to internalize stress. The swings in cortisol (a stress hormone), variances in gut perfusion, and heat generated by high workloads eventually show up in the gut. For working horses, the opportunity for overgrowth of bad or pathogenic bacteria can result from all those circumstances. On the other end, think of foals. The first few days of life are hard enough trying to establish a functional immune system and gut microbial environment. It is a delicate balance trying to populate and maintain the good bacteria, while fending off an overgrowth of bad bacteria which feed on the same nutrients. In either case, maintenance of good versus bad has many outside forces we are either directly responsible for or truly have little control over. Therefore, the supplementation of beneficial, good bacteria is something we must not overlook in the prevention of disease.

In the treatment of disease, it is even more important because by definition we are already behind. We are on the downhill side of a battle we do not want to lose.  Many so-called bad bacteria are opportunistic pathogens, meaning they are waiting for the optimal conditions for them to take over the system. When the cat is away the mice will play, right? Intestinal infections such as Salmonella and Clostridium are well known for a reason. Sometimes these bacteria take over from a weakened immune system due to a generalized disease or infection, but we must also and always be cognizant of what we as owners and veterinarians can do with the use of antibiotic medications when we treat infections. 

Antibiotic medications, whether given intravenously, intramuscular and especially via oral route have the capability of killing good bacteria just as they can the bad ones causing disease. Antibiotic-induced diarrhea is a real thing, and depending on the antibiotic of choice, it is much easier to induce than we care to admit. A common and wise practice I will use when administering certain, and especially long-term, antibiotics is to give a probiotic during and after the completion of a prescribed course of treatment. 


Focusing on times of stress is an excellent way to identify times when your horse’s gut health is at higher levels of risk. As Dr. High mentioned, we are often the source of our horse’s stress. Travel, competition and farrier visits are just a few of the situational stressors that we impose on our horse. There are also environmental stressors such as extreme temperatures, diet changes or disease exposure that we need to be aware of. All stressors can impact gut health, making the feeding of an effective probiotic a good choice.

Question 3. What should you look for in an effective probiotic?

Dr. High:

True story — so a week ago, I was at a big feed and tack store and thought I’d take a look at what probiotics were on the shelf. One of the smaller sections of the store had five different probiotic products for sale. I had to walk past hundreds of choices for grooming, joints supplements, and horse cookies to find what I wanted. Now I am standing there thinking, “Which one would I buy if I really didn’t know much about probiotics?” Unfortunately, like so many things in the world in general, it comes down to marketing. Well, marketing doesn’t always fix horses, so here’s what I look for. 

There are long-standing products available that are what I consider “large animal” probiotics — not species specific. Will what works for a cow or goat work for your horse? Maybe, but I am not willing to risk being the one to find out it doesn’t.  Therefore, I choose an equine-specific product. So, that eliminated three of the choices. Where do I go from there? I want two things. I want a probiotic that has a specific yeast culture in it called Sacchromyces boulardii. In my experience it has a tremendous record of safety and efficacy in clinical practice over many years. The other thing I want is for what is printed on the label to actually be in the syringe of product and be viable when I use it. So, now I am down to one. Problem solved, but I knew what I was looking for. Probiotics are tremendously useful products, but they are not unlike any other substance we put in our horses. We need to know why we are using them, and what really is in them to have the greatest success in our efforts.    


There are a variety of different probiotics on the market, and each has its own mode of action and benefit. Some are focused only on improving digestion, and others, such as the Bacillus subtilis PB6 found in CLOSTAT®, help to reduce the number of pathogenic bacteria in the gut. This allows for other prebiotics and probiotics in the horse’s diet to be more effective.

Regardless of why or how the probiotic is being fed — paste, feed or supplement — there are three things that I remind horse owners to look for:

  1. Proven survivability. As mentioned previously, probiotics are living organisms and need to be able to reach the gut alive in order to benefit your horse. They need to survive pelleting and exposure to feed additives and stomach acid.  
  2. Proven mode of action. I look for equine-specific data. Do you know exactly what the probiotic is doing and how it is doing it? You want to be sure of what you’re feeding and how it is benefiting your horse.
  3. Proven safety. Do you have data to support that this probiotic is safe to feed to horses?

It may be a lot to consider, but it’s important to meet these three criteria or you may just be wasting your time and money on an ineffective probiotic.

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