The Equine Intestinal Microbiome

The intestinal microbiome is trending, and judging by interest in pre- and probiotics it’s a rather longstanding interest too. Research has actually generated quite a lot of interesting information recently but we are light years away from really understanding how the teeming microbial population in the gut can interact with the horse’s body at large.

The composition of an individual’s microbiome is as unique as a fingerprint, complicating efforts to try manipulating it in ways that are deemed to be healthful [electron microscopic image of bacteria]

Some bacteria, like Salmonella, Shigella and certain strains of E.coli or Clostridia, are known to directly cause disease and we want to avoid them. For the vast majority though, their functions in fermentation of various types of equine foods is understood but any other effects are not well described and what’s good for GI and general health in a dog or human might not be in a horse.

Research to date has shown the three major bacterial phyla in the hind gut, in descending order, are Bacteroides, Firmicutes (some studies show Firmicutes more abundant) followed by Fibrobacteria or Verrucomicrobia in most horses, with many different genus and species within them. However, there is tremendous individual variation by sex, breed, diet, geographical location, level of exercise and things like antibiotics. Because of this, it is extremely important that strict experimental conditions be used to minimize those influences when trying to determine any changes present in a disease state.

There is also limited information to be gained from manure. The microbiome of the cecum and ventral colon are similar but very different from the dorsal colon and small colon. Comparing information between studies and even samples within any given laboratory is  hindered by alterations that occur due to sample handling [Beckers et al 2017].

An area of high interest now is any connection with obesity since mouse and human studies seem to show a clearly different intestinal microbiome in the obese. A few  studies detected some changes in horses but they used subjects not standardized for breed, location and diet. In two well controlled recent studies, Morrison et al 2018 from UK and Coleman et al 2019 USA showed no differences between normal weight and obese horses in their bacterial phyla. Unlike in humans and mice, bacterial diversity is higher in obese horses. Some studies showed an increase in isolated genera like Verrucomicrobia or Pseudoflavonifractor in obese horses but no two studies showed the same thing and others showed no significant differences.

What does all this mean? For one thing, it’s complicated! Even when a pattern is found, as in people and mice, it is still unknown what is cause or effect, chicken or egg. It also  means that services cropping up that claim to diagnose health issues in your horse from a fecal microbial profile have no solid scientific ground to stand on.

There are several companies I know of, in UK, USA, AU, offering fecal cultures or fecal genetic  material profiling which claim to identify disease risk. Among the things claimed to be detected are influences on metabolism, gut wall renewal, dysbiosis/colitis, gut wall integrity linked to diet or “stress”, inflammation/immune function and bloating.  Claims are made that they can identify changes in your horse linked to disruption in those functions, as well as outlandish advice such as supplementing your horse with vitamins and minerals will kill off beneficial microbes.

These tests are very expensive, as are the variety of prebiotics, herbs and anti-acidity products they sell to go along with them and cure the problems.  Don’t be taken in or your horse may suffer along with your wallet.

Eleanor Kellon, VMD


About Dr. Kellon

Graduate of University of Pennsylvania Veterinary School. Owner of Equine Nutritional Solutions,, industry and private nutritional consultations, online nutritional courses. Staff Veterinary Expert at Uckele Health and Nutrition.
This entry was posted in Equine Nutrition and tagged , , , , , . Bookmark the permalink.

1 Response to The Equine Intestinal Microbiome

  1. Julieanne Tester says:

    So glad I read this I was about to waste my money!

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