The Importance of Equine Hindgut Microbes

The equine digestive system is rather unique amongst other herbivores. Known as “hindgut fermenters”, horses have evolved to digest the most fibrous portions of their feed in their cecum and large colon, which are near the end of their digestive tracts. This differs from many other herbivores, like cattle, who have large multi-chambered stomachs (rumens). These animals ferment and digest fiber in their foregut.

Like other herbivores, the breakdown of a horse’s feed is aided by billions of bacteria, protozoa, and fungi, which we commonly refer to as “gut microbes”. Understanding the role gut microbes play in equine digestion is important because they are critical to keeping horses healthy. For instance, when the microbial population balance is upset, it can lead to many common health ailments.

Where Are the Horse’s Gut Microbes?

Before jumping into the specifics of the horse’s gut microbes, it is worth a quick review of how horses digest their feed. Our article How Your Horse’s Digestive System Works goes into more specifics. Briefly, as a review:

  • Stomach. Unlike other herbivores, the equine stomach is much smaller, at only 10% of the total volume of the digestive tract. Its role is to mix in acid and enzymes to begin the breakdown of feedstuffs, which are quickly passed on to the small intestine. Due to the high acidic nature of the stomach, there is little to no microbial action here.
  • Small intestine. Most of the absorption of available nutrients takes place in the horse’s small intestine. Like the stomach, there is little to no microbial breakdown of feedstuffs here, but rather, feed is broken down by digestive enzymes. 
  • Cecum. The undigested portion of a horse’s diet first enters the hindgut through the cecum. This is a large vat that acts like a cow’s rumen. Here, the horse’s hindgut microbes begin to ferment any undigested feed, usually the fibrous portion of forage.
  • Large colon. After spending considerable time in the cecum, feed is passed to the large colon for further microbial fermentation and absorption of nutrients.

The important gut microbes involved in digestion are located in your horse’s hindgut.

The Role of the Horse’s Hindgut Microbes

The forage (hay/pasture) that a horse eats is made up of cellular contents and a cell wall. The cellular contents are mainly digested by enzymatic action and absorbed in the stomach and small intestine. Here, the nutrients provided by the cellular contents are protein, starch, sugars, fats, vitamins, and minerals.

The main components of the forage cell wall are cellulose, hemicellulose, and lignin. These are usually resistant to any digestive enzymes and provide little to no nutritional value in the stomach or small intestine of the horse. However, with the assistance of the hindgut microbes, the nutritional value of the cell wall to the horse is quite high. The billions of microbes in the horse’s hindgut help break down the cell wall contents by fermentation. Through this fermentative process, volatile fatty acids (VFAs) are produced, which are then absorbed by the horse. The most common VFAs are acetate, butyrate, and propionate. The single most important factor in this fermentation process is that the VFAs provide up to 70% of a horse’s daily energy supply. This means that the VFAs provided by microbial fermentation of forage in the hindgut are the single most important source of energy for the horse. Other nutritional benefits of the hindgut microbes include the production of B vitamins.

There are many types of microbes in the hindgut. Here are just some of the types of microbes and species found:

  • Bacteria, Ruminococcaceae, helps with cell wall degradation.
  • Bacteria, Fibrobacteaceae, helps with cell wall, sugar, and starch degradation.
  • Bacteria, Streptococcaceae, helps with starch utilization.
  • Bacteria, Lactobacillaceae, produces amino acids and lactic acid. 
  • Bacteria, Acidaminococcaceae, ferments fiber.
  • Bacteria, Lachnospiraceae, helps with cell wall degradation and fermentation.
  • Fungi, Neocallimastigaceae, helps break down cellulose.
  • Protozoa helps break down hemicellulose and pectin.

While knowing each individual microbe is less important, it is noteworthy that there is a diverse range of microbes found in the equine digestive system. This will help in understanding what we feed or how management can affect and alter the microbial population in the horse’s gut.

Keeping the Horse’s Hindgut Microbial Population Healthy

There are many equine health issues that can be traced back to hindgut health and the makeup of a horse’s microbial population. An unhealthy hindgut microbial population can lead to:

  • Hindgut acidosis
  • Laminitis
  • Colic
  • Colitis

The most common cause of an unhealthy microbe population is a shift in the hindgut’s microbial population, which can be due to grain overload or a sudden dietary shift. In the case of grain overload, this can be caused by feeding too much feed during a single meal or the horse gains access to the feed room. This starch/sugar overload leads to lactic acid-producing bacteria (i.e., Streptococcaceae) proliferating and killing off other important microbes (i.e., Fibrobacteaceae). This sudden increase in lactic acid results in a lowering of the hindgut pH from a neutral range of 7, to a low of 4, and leads to a host of issues.

The single most important factor in maintaining hindgut health is providing enough high-quality forage to your horses. Providing enough forage (daily) will help the horse in maintaining the right balance of microbes. We have also detailed, in greater depth, how best to avoid an unhealthy microbe population in our Supporting Your Horse’s Hindgut Health article. Briefly, tips include:

  • Feeding pre- and probiotics to support a healthy population of hindgut microbes.
  • Feeding at regular intervals at no less than 2x per day, optimal 3-4x per day.
  • Never feed more than 0.5% of your horse’s body weight in feed at any single meal (i.e., 1000 lb horse = 5 lb feed per meal).
  • Make any changes to a horse’s feed slowly. This can be done safely over 2-3 weeks. 
  • Ensure a horse’s feed is properly secured.

Take Home Message

Maintaining a healthy hindgut microbial population for a horse is critical to their overall health and wellbeing. It is one of the major reasons horse diets are carefully managed. However, having knowledge on the purpose of the hindgut microbes and how they can be managed will help you in keeping your horses healthy and happy. If you have any questions or concerns about what you are feeding your horses, please feel free to contact us for a free consultation.


Venable, al. (2016). Role of the gut microbiota in equine health and disease. Animal Frontiers. 6:43-9.

Kauter, A. et al. (2019). The gut microbiome of horses: current research on equine enteral microbiota and future perspectives. Animal Microbiome: 1:14.

Article By: Chris Mortensen, Ph.D.
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