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The Microbiome

As they uncover the microbes in the ­intestine—which is as daunting a task as decoding the equine genome—­researchers are simultaneously attempting to determine what functions each serves. Currently, they believe on the whole the equine microbiome is responsible for:

  • Fermenting fiber in the hindgut to produce short-chain fatty acids (SCFAs), primarily propionate and butyrate, that the horse’s body absorbs into the bloodstream from the GI tract and uses for energy;
  • Boosting the horse’s immune ­system;
  • Producing antimicrobial products to control populations of pathogenic (disease-causing) microbes;
  • Physically excluding pathogens; and
  • Inhibiting the production and absorption of bacterial toxins (e.g., those produced by Clostridium difficile, a common cause of diarrhea in horses).

The Microbiome during Disease, Stress

The intestinal microbiome is comprised of quadrillions of microbes, and keeping them all happy is imperative to horse health. In adult horses, colic and colitis, laminitis, foal heat diarrhea, and equine grass sickness are the most notable consequences of disrupting the equine intestinal microbiome.

To help characterize the exact changes in the equine intestinal microbiome under certain conditions, one research group, including Christopher Proudman, MA, Vet MB, PhD, Cert EO, FRCVS, of the equine division of the University of Liverpool’s Department of Veterinary Clinical Sciences, in the United Kingdom, collected and analyzed samples from the large intestines of horses:

  1. Maintained on pasture;
  2. Consuming a concentrate diet; or
  3. Consuming a concentrate diet and diagnosed with simple colonic ­obstruction and distension (SCOD), a prevalent form of the diet-induced intestinal disease.

Keeping the Microbiome Happy

One potential way to maintain the equine intestinal microbiome’s health and integrity is through probiotic administration. Probiotics are “direct-fed microbial,” or live yeast and/or bacteria believed to help maintain or restore the health of the intestinal microbiome. Probiotics’ potential mechanisms of action include boosting the horse’s immune system, producing some antimicrobial products, excluding disease-causing microorganisms, and inhibiting bacterial toxins. Examples of probiotics include bacteria and yeast such as Bacillus subtilis, Bacillus licheniformis, Saccharomyces cerevisiae, Lactobacillus acidophilus, Enterococcus faecium, Lactococcus lactis, and Bifidobacterium longum, among others.


“A further understanding of the horse’s  intestinal microbiome will help (owners and veterinarians) manage these animals during a critical part of their lives. ”

Dr. Scott Weese





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