Research shows slight shifts in the intestinal microbiome can have far-reaching effects

Scientists are slowly but surely unveiling the secret workings of the equine intestinal microbiome. Although it might sometimes seem more slow than sure, we must appreciate that studying the microbes that reside in the large intestine and cecum can be like shining a flashlight onto the surface of the Atlantic Ocean at 41.726931° N, 49.948253° W, hoping to study the Titanic.  

The Healthy Intestinal Microbiome

Originally, researchers believed the sole, or at least primary, role of the intestinal microbes was fiber fermentation. As we know, horses cannot digest the fiber that makes up the bulk of their diet with teeth, saliva, and gastric acids alone. Instead, they rely on the bacteria within the large intestine to ferment those feedstuffs and produce volatile fatty acids—short-chain fatty acids the horse then uses for energy.

Now, we know the intestinal microbiome comprises far more than just fiber-fermenting bacteria. In fact, the term microbiome refers to all the microbes and their genes that call the hindgut home, including bacteria, fungi, viruses, and protozoa.

“The gut microbiome is linked to so many parts of what we think of as host health,” says Grace Vaziri, a PhD candidate in ecology and evolutionary biology at the University of Connecticut, in Storrs. “In addition to its role in digestion, the microbiome influences immune system development and maturation. As well, gut microbes help maintain a constant gut-brain conversation going based on the chemical byproducts they produce during digestion.”

It is widely accepted that horses have a “normal” population of microbes in a healthy intestinal tract. This might vary somewhat from one horse to another but, overall, healthy horses generally have the same core microbiome.

According to a 2023 review article by Carolyn E. Arnold, DVM, PhD, Dipl. ACVS, published in Veterinary Clinics of North America: Equine Edition, healthy horses have about 17 to 20 different bacterial phyla in their fecal microbiome, which is reflective of the large colon (it’s difficult to impossible to sample the hindgut microbiome in the live horse), but three main phyla tend to be the most common in all equine microbiome studies: Firmicutes, Bacteroidetes, and ­Verrucomicrobia.

The Firmicutes, the most predominant phyla, play important roles in degrading complex plant materials. This phylum includes bacteria in the Lachnospiraceae and Ruminococcaceae families. These bacteria produce volatile fatty acids essential for equine health.

Bacteroidetes also ferment fiber to produce volatile fatty acids, while the Verrucomicrobia help maintain the gut barrier between cells lining the intestinal wall and the contents of the intestinal tract