The Equine Intestinal Microbiome

Keep the horse’s microbiome healthy by mimicking the lifestyle maintained by wild horses.

The Equine Intestinal Microbiome
It’s important to focus on developing feeding strategies that promote a healthy microbiome. | iStock

The microorganisms making up the intestinal microbiome do more than just produce energy for the horse. The microbiome is like its own organ that is crucial for horse health, said Tania Cubitt, PhD, an equine nutritionist with Performance Horse Nutrition, in Jeffersonton, Virginia.

During her 2022 EquiSummit virtual presentation, Cubitt highlighted some of the intestinal microbiome’s key known roles, including:

  • Harvesting nutrients and extracting energy from the diet.
  • Resisting colonization of pathogens (disease-causing organisms).
  • Developing the immune system.
  • Removing toxic compounds from the host.

“The microbiome, which includes all the different microbes in the horse’s hindgut, is absolutely critical for everything that happens in the horse,” emphasized Cubitt. “The microbiome can be affected by a large variety of factors. Anything that stresses a horse can negatively impact the microbiome.”

Stress typically includes anything a “wild” horse would not do or experience.

“A wild horse’s lifestyle and diet are the gold standard for normal, healthy horses,” she said. “To optimize equine health, we want to mimic natural behavior and natural gut health.”

In the wild, horses consume a wide variety of forage, live in herds, and move around while grazing continuously with their heads down.

“Compare this to even the most spoiled domesticated horse,” Cubitt said. “Even with deep bedding, a well-lit warm stall, and high-quality feeds, domesticated horses are often stalled alone, with their feed bucket at chest height from which they are fed meals, and have restricted exercise. Just living this way causes stress, which in turn, is not ideal for a healthy intestinal microbiome.”

Study results show increased stress decreases microbial diversity, defined as the type and numbers of microbes, such as bacteria, in the microbiome. Two of the most common bacteria are Firmicutes, which produce volatile fatty acids like butyrate that horses use for energy, and Bacteroidetes that break down indigestible fiber.

“Domestication, diet, body condition, medications, and more can all decrease diversity within the microbiome, which can have far-reaching effects,” warned Cubitt.

Cubitt said when Firmicutes populations decrease, butyrate levels also decrease. Butyrate has a protective level on the cells called colonocytes, found in the wall of the gut. Those intestinal cells are held together by tight junctions that create a barrier between intestinal tract contents and the horse’s bloodstream. During times of stress those tight junctions break down, and the gut becomes “leaky.” When this happens, toxic materials and bacteria can flow freely into the horse’s bloodstream.

“As a result of leaky gut, the horse suffers from system-wide, low-grade, chronic inflammation,” Cubitt said. “These horses tend to present with overall soreness, changes in behavior, and allergy-like symptoms.”

She advised focusing on developing feeding strategies that promote a healthy microbiome while simultaneously discouraging the growth of pathogenic bacteria.

“The microbiome is the link between nutrition and health,” she emphasized.

In addition to standard recommendations for feeding the intestinal microbiome to better mimic the diets of wild horses, Cubitt mentioned the possibility of feeding horses butyrate.

“The microbes that produce butyrate, such as Firmicutes, seem to ‘go down’ first when a horse becomes sick or diseased,” she explained. “Butyrate induces the production of host defense peptides that simulate the development and repair of the intestinal tract through an increase in cell proliferation. Butyrate is really important, which makes nutritionists wonder if we can add butyrate to horses’ diets to keep the colonocytes and tight junctions healthy. Potentially, yes, we can.”

Cubitt concluded that any therapy aimed at microbiome restoration represents the next frontier in equine gastrointestinal health and should, therefore, be a focus of future research.


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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