Manipulating the Equine Microbiome

Recent study results suggest dietary changes can alter horses’ intestinal microbiome to their benefit.

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horse eating from haynet
Making changes to the horse’s diet influences their microbiome. | iStock

In 2018, Costa and Weese suggested manipulation of the equine intestinal microbiome is a promising avenue for improving horse health and potentially enhancing animal performance. This holds true today, yet much of the intestinal microbiome remains relatively unchartered. Without understanding what a healthy intestinal microbiome “looks like,” it is impossible to begin manipulating the resident microbiota to provide precision nutrition.

Indeed, Costa and Weese wrote, “It is important to have an understanding of the normal microbiota to enable assessment of abnormal. However, what truly constitutes normal is elusive because there can be marked variation, and a plethora of factors can influence the composition of the microbiota in healthy horses. Normal may vary between regions, ages, management systems, and potentially even breeds; therefore, broad assessment of populations is required to have an understanding of normal.”

While each individual horse has its own unique microbiome, researchers are discovering that horses of the same breeds and/or management systems and herds might share similarities.

What Bacteria Are in the Equine Intestinal Microbiome?

In two recently published studies, researchers examined what constitutes a normal intestinal microbiome. In the first, Ayoub et al. compared the intestinal microbiomes of four populations of horses: one herd of university teaching horses and one group of privately owned horses in Ontario, Canada, and one herd of teaching horses and one group of privately owned horses near Gainesville, Florida.

In that study, the most abundant phyla of bacteria were Firmicutes and Bacteroides, followed by Verrucomicrobia, Proteobacteria, Spirochaetes, and Fibrobacteres. Five highly abundant families of bacteria within those phyla were Lachnospiraceae, Ruminococcaceae, and Clostridiales (each from the phylum Firmicutes), Bacteriodales (from the phylum Bacteriodes), and Treponema (from the phylum Spirochaetes).

These bacteria appear “particularly important in maintaining gastrointestinal tract health in horses and are likely a major component of the core microbiota,” the researchers wrote.

In a second study published this year, Wen et al. compared the intestinal microbiome of three horse breeds: Thoroughbreds, Mongolians, and a cross between the two. The predominant phyla found in fecal samples collected from those three groups were similar: Firmicutes, Bacteroidetes, Spirochaetes, Proteobacteria, Verrucomicrobia, and Fibrobacteres. These were also similar to the major phyla found in all four populations of horses reported by Ayoub et al.

These phyla were also found in the human intestinal microbiome, with Firmicutes and Bacteroidetes representing about 90% of the gut microbiota (Rinninella et al. 2019).

These results show the equine intestinal microbiota is vast and varied. “The Firmicutes phylum is composed of more than 200 different genera, such as Lactobacillus, Bacillus, Clostridium, Enterococcus, and Ruminicoccus,” said Tania Cubitt, PhD, a nutritionist with Performance Horse Nutrition, based in Weiser, Idaho. “The Clostridium genera represent 95% of the Firmicutes phyla. The Bacteroidetes phylum consists of predominant genera such as Bacteroides and Prevotella, which are probably not as well-known to horse owners as the Firmicutes.”

This information also shows not all Clostridium spp are as pathogenic (disease-causing) as once thought.

What Do These Bacteria Do?

The intestinal microbiome’s main roles include harvesting nutrients and extracting energy from the diet to produce short-chain fatty acids (SCFAs), resisting the colonization of pathogens, and developing the immune system, said Cubitt.

The intestinal microbiome also plays an integral role in maintaining the integrity of the intestinal wall.

For example, the short-chain fatty acid butyrate “supports the gut barrier, which keeps bacteria and other microbes from entering the blood,” Cubitt said. “In turn, this helps control inflammation and even aids in preventing disease.”  

In terms of the microbiota itself, what do some of the above-listed microorganisms do? In their study, Wen et al. provided examples:

  • Lachnospiraceae and Ruminococcaceae (Fibrobacteres) both hydrolyze starch and other carbohydrates such as cellulose in the hindgut to produce SCFAs, including butyrate;
  • Ruminococcaeceae produce SCFAs that have immunomodulatory and anti-inflammatory effects. Some of those SCFAs may also promote glucose uptake and metabolism in skeletal muscle; and
  • The butyrate produced by fibrolytic bacteria can improve the efficiency of energy metabolism in muscle fibers.

Altering Diet Might Benefit Horses

Understanding the key players in the intestinal microbiome is an important step to maintaining health, but Wen et al. suggest we can do more. They say manipulating the intestinal microbiome might also enhance equine performance.

For example, the Mongolian horses in their study had a significantly higher ratio of Firmicutes to Bacteroides compared to Thoroughbreds. The researchers suggested Mongolian horses could therefore absorb heat more efficiently than Thoroughbreds, making them more cold-resistant.

In contrast, the Thoroughbreds’ feces were richer in certain families of bacteria than the Mongolian horses. Those bacteria produce SCFAs confirmed to “promote glucose uptake and metabolism in skeletal muscle” and “improve the energy metabolism efficiency of muscle fibers.”

Thus, altering specific bacterial populations not only at the level of the phyla but also the genus and species by changing the composition of the horse’s diet could help optimize their health, well-being, and performance. However, more research needs to be done to identify specific forage, concentrate, and supplement adjustments and how they can benefit the horse most.

Ayoub, C., Arroyo, L. G., et al. Fecal Microbiota Comparison between Healthy Teaching Horses and Client-Owned Horses. 2022. Journal of equine veterinary science.

Wen, X., Luo, S., et al. Variations in the fecal microbiota and their functions of Thoroughbred, Mongolian, and Hybrid horses. 2022. Frontiers in Veterinary Science


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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