EQUUS ‘Farm Calls’ episode 10: The equine microbiome

Dr. Marcio Costa helps us understand how the microbiome affects our horses, both positively and negatively.

“The microbiome is all those microscopic organisms that inhabit our body,” said Dr. Marcio Costa, an assistant professor in the department of Veterinary Biomedical Sciences at the University of Montreal. He said they are mostly bacteria, but also has fungus and other organisms. “They play an important role in keeping us healthy.”

He said most of the time when we think about bacteria, we think about “bad guys” that cause disease. “The majority are good and necessary for us,” he said.

The same is true of our horses.

In this edition of the EQUUS Farm Calls podcast, Costa helps us understand how the microbiome affects our horses both positively and negatively. He also talks about:

  • What is a microbiome?
  • What is an intestinal microbiome?
  • Why is understanding intestinal microbiomes so important to horse health?
  • What do horse owners need to know about a healthy equine intestinal microbiome?
  • Recent research

Many Microbiomes

Each part of a horse’s body has a distinct microbiome—the skin, the oral cavity, the vaginal area and the gastrointestinal tract, to name a few.

“Bacteria regulate the immune system and protect our horses,” Costa said. He added that “Good bacteria help the horse absorb more nutrients [in the GI tract] than a horse without those good bacteria. The good bacteria protect against bad bacteria, so a population of good bacteria equals less diarrhea and malabsorption.”

The bacteria present in a horse can be changed. Antibiotics can kill good and bad bacteria, “… and if you kill the good bacteria, you allow the bad bacteria to proliferate and cause other issues,” noted Costa. Also, the diet you feed a horse can affect the microbiome in which bacteria flourish.

So how important are these little “bugs” to our horses? “We can kill the cecal microbiome, and that can cause laminitis,” said Costa.

Diversity Is Important

Costa mentioned that there is a lot of research on the equine microbiome now. “The way we treat horses means we change the microbiome,” he said.

Some research has looked at comparing the microbiomes of wild versus domestic horses, canines and birds, for example. Costa said that research has shown that the more diverse the bacteria, the better the animal’s health. “We need to learn how to live with those changes” and keep our horses microbiomes healthy, he said.

Most horse people know about foals eating their dams’ poop in order to populate their guts with the proper bacteria. That is just one way to manipulate the microbiome.

Others include giving probiotics, which are live bacteria that have the potential to cause benefit. Costa also talked about prebiotics, which are known digestible fibers that the host can’t digest, but the good bacteria can. “So, you are feeding the bacteria,” he explained. But he was quick to add that researchers don’t know which fiber targets specific bacterial species. “If we overdose prebiotics, we can change the microbiota in a negative way.”

With probiotic studies, he said some show benefits, and some show no differences. “We prescribe a lot of probiotics to horses with diarrhea,” noted Costa, adding, “There is a lot of research on this topic in humans.”


There is a process used in human and veterinary medicine to try and help correct problems with the GI tract microbiome. It is called fecal microbiota transplant (FMT).

Costa said literature has shown that FMT can prompt improvement in a horse with digestive tract issues. But he also said it is frustrating because there is some disagreement in literature, and there isn’t a clear answer.

He said we have to remember that FMT can transfer bad bacteria along with good bacteria. “That’s why you have to have strict donor selection,” he said. But even that can be a problem because some of those horses have transient shedding of problem bacteria. “We spend a lot of money testing donor horses,” Costa said.

The Future

Costa said human doctors and researchers are trying to develop a “super-probiotic” for humans.

Costa said for horses, “We want to develop products that are medicines, that maybe have 35 species of bacteria to create an ‘ecosystem’” for the horse’s gut.”

This episode was brought to you by our partners at Farnam, the maker of Cough Free Equine Respiratory Health Pellets. When your horse needs some extra respiratory help, trust Farnam, Your Partner in Horse Care for over 75 years.




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