Your horse just finished a round of antibiotics. What’s next? Here’s how a natural approach can help restore him to good health.

Antibiotics are used very liberally in the horse world, and they may be needed in many cases. However, it’s important to realize they do some damage to the gut. The good news is that there are many natural ways to heal the gut, repair the immune system damage, and improve the long-term health of the horse and his microbiome.


The intestinal tract contains bacteria and many other microbes (the microbiota) designed to digest food, manufacture vitamins and make minerals available. The genetic makeup of these microbiota is called the microbiome. The microbiota grow on dietary fiber called prebiotics in the digestive tract, not on the intestinal wall. The populations of microbiota are quite variable between horses, even those kept on similar feeding programs. Because they reproduce rapidly, microbial populations are susceptible to changes in the diet and environment.

When digestive tract microflora become unbalanced, the bacteria are not present in the correct proportions and incomplete digestion occurs. With incomplete digestion and poor quality feeds, the pH can become altered, leading to the migration of bacteria into inappropriate places, or to an overgrowth of microbes that are not supposed to be in a certain location.

Antibiotics damage the microbiota by killing all microbes indiscriminately. In the process, the gut wall also becomes inflamed, creating a “leaky gut” situation. When this occurs, the gut wall actually becomes leaky and compounds can pass through it into the body in a form that is inappropriate or even toxic.


Microbes play a variety of roles in the immune function of the gut. The good ones directly compete for space and can overcome pathogenic bacteria by their physical presence. They can also prevent pathological bacteria from entering the lining of the gut. They have been shown to play a direct role in the immune system in ways we are just beginning to understand.

When we give antibiotics, we are trying to kill off the bad bugs that could overwhelm the immune system, leading to an infection. This could be an infected wound or something like Lyme disease. We tend to just assume the body will recover and be healed; however, once that microbiome is damaged, the immune system is also damaged. In some cases, in animals with a strong microbiota and immunity, the immune system recovers, and the horse stays healthy. In many cases, the immune system and microbiota never recover and the immune system weakens over time, increasing the risk of health problems. In the case of Lyme disease and similar deep chronic infections, the organism continues to deplete the immune system and the horse never seems to recover properly.


Repairing the gut microbiota is the most important thing you can do for your horse after a course of antibiotics. It is also important if your horse has any chronic diseases (skin issues, colic, allergies, etc.), since we often do not know our horse’s lifetime exposure to antibiotics. It’s possible that as a foal, she was treated for pneumonia; or if there is a scar anywhere, it’s likely antibiotics were used liberally to heal that wound.

A combination of healthy feeds, pre and probiotics, as well as some herbs and nutritional supplements can repair the gut wall and immune system.

Horses fed a forage-based diet tend to have a healthier and broader population of microbes than grain-fed horses. Switching to a whole food diet instead of processed feed will make a big difference. Unless you have a hard keeper that needs a lot of calories, most horses do well with a moistened hay pellet mixed with a vitamin/mineral supplement as their “feed”. They think they are getting a meal in their bucket, and you can add any other supplements you wish.

Prebiotics are short chain fibers that the microbiota grow on. One of the most common is inulin. It’s found in the plant chicory and can be fed as a concentrated powder (20 g to 30 g twice a day), if you do not have much chicory growing nearby. Others prebiotics include fructooligosaccharides (FOS), beta-glucans (from mushrooms or foods like oats and barley) and mannan-oligosaccharides (MOS). These can be found in some of the probiotic supplements on the market.

Prebiotics can also come in the form of compounds from humus, such as fulvic and humic acids. These come from the soil; the microbiota that live and reproduce in the gut are similar to those that naturally occur in the soil, as opposed to those we commonly supplement. S, these soil compounds help support the microbiota.

Herbs and plants
Herbs can be added for a variety of reasons because they contain many compounds that help heal the gut wall as well as supply prebiotics. Diverse pastures supply a variety of plants and herbs that the horse can select as needed. If that is not possible, try planting a patch of herbs for your herd to graze for short periods, or add seeds to your pasture to increase plant diversity. Plant small patches in areas away from high traffic paths so the herbs have a chance to grow. You can also grow plants in your own organic garden with great soil microbes, and feed carrots and other root crops without washing the soil off.

Other herbs such as marshmallow, aloe, fenugreek, chamomile, dandelion and ginger can all be used to help heal the gut wall. Slippery elm is commonly used, but is an endangered herb, so if it is used, it needs to be harvested ethically. The company you buy from should be able to confirm the sourcing.

Probiotics are always useful as part of the damage control and repair process. During antibiotic usage, the drugs kill off the probiotics you are adding to your horse’s feed. However, it is still beneficial to feed them, while knowing that all you are doing is some damage control. The real repair comes after the antibiotics are finished. If you can feed probiotics at a different time than the antibiotics, that’s great, but it’s not always possible in boarding situations or at home when you have to go to work and feed twice a day. Probiotic supplements primarily help create a positive environment for the microbiota to thrive, rather than replace the damaged bugs.

Probiotics should be free from additives, fillers, sugars and preservatives. If possible, it helps to have them microencapsulated to prevent breakdown on the way to the small and large intestines, though products without microencapsulation do help.

Other nutrients
Many additional nutrients help heal the gut wall and repair the gut’s immune system. Glutamine is an amino acid that is fuel for the enterocytes (the cells that make up the gut wall), so the addition of 20 g to 30 g twice a day can be helpful, especially if the horse has been ill and wasn’t eating well during the antibiotic usage. It can also be helpful in lower doses as part of a supplement.

Colostrum is an important nutrient that acts directly on the immune system in the lining of the gut wall. Colostrum has become very popular but should only be used if it is sourced from grass-fed cows that are not stressed. Commercial dairy cows are under a huge amount of stress and their colostrum is not as healthy for the immune system.


Repairing the horse’s gut after antibiotic use is important. Gut health is really at the center of general health; research is now proving that without a healthy microbiome, overall body health suffers. It takes a minimum of three months to heal the gut after a short course of antibiotics, and much longer than that after months of antibiotics, or after repeated bouts of antibiotics, which are given to many Lyme and chronic disease sufferers. However, if you take the time and money to repair your horse’s gut after antibiotic usage, you will save both aggravation and extra cost in the long run, and have a healthier horse.

Joyce Harman graduated in 1984 from Virginia Maryland Regional College of Veterinary Medicine. Her practice is 100% holistic, using acupuncture, chiropractic, herbal medicine and homeopathy to treat horses and enhance performance for those with a variety of chronic conditions. Her publications include the Pain Free Back and Saddle Fit books, the only ones written independently of a saddle company. She maintains an informative website at and