How the Horse’s Intestinal Microbiome Works

For any horse with appetite, appearance, or attitude issues, start by addressing the microbiome.

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hay and grain
The microbiome takes up to three to four weeks to fully adapt to a diet change. | Anne M. Eberhardt/The Horse

The equine intestinal microbiome’s wide-reaching effects on the horse’s overall health can be difficult to comprehend. After all, quadrillions of microbes reside within the intestinal microbiome, each playing various roles in energy production, immunity, disease protection, and as an endocrine (hormonal) organ.

To help owners appreciate the world hidden within a horse’s hindgut, Jyme Nichols, PhD, Director of Nutrition for Bluebonnet Feeds and Stride Animal Health, gave a presentation on the equine intestinal microbiome during the 2022 Kemin EquiSummit, held virtually May 25-26. Nichols compared the microbiome to an ecosystem one would find above ground, such as animals in a forest with rocks and a pond.

“The microbiome is like other biological communities in which organisms interact with one another and their physical environment, both living and nonliving,” she explained.

In the intestinal microbiome the living organisms that make up the community within the ecosystem are bacteria such as lactobacilli, streptococci, and enterococci, as well as yeast/fungi. These organisms, said Nichols, “eat” carbohydrates, metabolize them, then produce volatile fatty acids the horse relies on for energy.

Like a forest with birds, insects, and mammals, the members of the horse’s microbial community are specifically tailored to survive in certain environments. For example, you wouldn’t take a bird from a forest in northern New York and let it free (and expect it to thrive) in Brazil. Further, while the horse’s microbial community can shift and adjust to a certain extent to changes in the ecosystem, you should never expect fiber-loving microbes to thrive in a starch-laden environment.

“In the case of the intestinal microbiome, changing ingredients in the diet, adding supplements, or altering the type and amount of grain or forage alter the environment, which means the community—the microbiota—must adapt,” Nichols explained.

Such adaptations in the community mean certain bacteria become more prominent and others less so. For example, if a horse consumes more fiber, then fiber-fermenting bacteria could increase in abundance as a result.

In extreme situations “natural disasters” can destroy the ecosystem. In the forest analogy, this could be a hurricane or volcano that wipes out most of the living community. The community might ultimately recover, but it could take days, weeks, or even years.

“In some situations, it is impossible for the community to recover,” Nichols warned.

She said a “natural disaster” in the intestinal microbiome could ensue after selling a horse that is used to a 100% pasture diet to an owner who feeds sweet feed three times a day without offering any forage.

“This would be akin to a wildfire in a forest,” said Nichols.

In this scenario the horse is at risk of colic due to the massive change in the microbiome community.

Nichols provided additional information on “natural disasters” in a horse’s intestinal microbiome:

  • The microbiome community takes up to three to four weeks to fully adapt to even a benign change in diet. “This holds true even after introducing a new load of the same type of hay the horse normally eats or adding in a new nutritional supplement, not just after adding or removing concentrates,” said Nichols.
  • Travel is also stressful and can change the microbial community. As few as one to two hours of travel is all that’s needed to induce these changes. And, said Nichols, even the horses left at home experience stress due to the change in social dynamics when a herdmate is trailered off. So, the remaining herd’s microbiome can also be altered.
  • Pharmaceutical drugs might, including nonsteroidal anti-inflammatory drugs (NSAIDs such as phenylbutazone, aka Bute), dewormers, antibiotics, and sedatives, might cause a shift in the microbiome.

“This is especially true if these medications are used often or off-label,” Nichols said.

“For any horse presenting with appetite, appearance, or attitude issues, start by addressing the microbiome,” said Nichols. “From nose to tail, the microbiome affects the overall well-being of that horse.”

Her two key tips for balancing the microbiome were:

  1. Offer plenty of good-quality forage, and only use grains to fill in nutritional gaps, and
  2. Support the microbiome with pre-, pro-, and postbiotics, especially during times of stress (i.e., transport, medications, change in ownership or herd dynamics).


Written by:

Stacey Oke, MSc, DVM, is a practicing veterinarian and freelance medical writer and editor. She is interested in both large and small animals, as well as complementary and alternative medicine. Since 2005, she’s worked as a research consultant for nutritional supplement companies, assisted physicians and veterinarians in publishing research articles and textbooks, and written for a number of educational magazines and websites.

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