A healthy equine gastrointestinal microbiome contains a diverse range of beneficial microbes that support digestion, immune function and nutrient synthesis.

Because horses are hindgut fermenters, a healthy microbiome is essential for overall wellness. Dysbiosis is defined as a microbial population that is unbalanced, dominated by harmful microbes, or has decreased numbers or diversity of organisms. By definition, dysbiosis also includes impaired function of the microbiome in individuals with intestinal tract disease. [20]

Horses with dysbiosis may develop excessive permeability of the intestinal barrier (sometimes referred to as ‘Leaky Gut‘), leading to colitis and increasing the risk of laminitis.

Some of the most common causes of alterations in the microbiome of horses include sudden diet changes, a diet that is high in rapidly fermented starches or sugars, stress, and use of medications or deworming drugs. However, many of these cause only transient changes in the gut microbiome and do not induce frank “dysbiosis” which, by definition, is only present when there is gastrointestinal disease. [20]

Horses with dysbiosis or other gut issues may exhibit a wide range of symptoms including digestive disturbances, weight loss, behavioural changes, and inflammation in the gastrointestinal tract.

Treatments for dysbiosis may include making changes to the diet of affected horses and replenishing the beneficial bacteria of the gastrointestinal system by feeding pre- and probiotics or transplanting fecal organisms from a healthy horse.

If your horse is affected by dysbiosis or other gut problems, submit their diet for analysis and our nutritionists can help you design a gut-friendly feeding program for free.

The Equine Microbiome

A properly functioning digestive system is essential to equine health and performance.

Research continues to highlight the link between digestive health and immunity, the neurologic system, and metabolism in horses and humans.

The equine gastrointestinal system contains thousands of different species of bacteria, yeast, fungi, and protozoa. [1]

To support optimal health, the microbiota should be dominated by “good” microbes that help to maintain a healthy gut and defend against “bad” microbes or pathogens.

The composition of the equine microbiome is influenced by multiple factors including genetics, diet, and environment. It varies significantly between horses.

A research study that evaluated the composition of fecal microbiota obtained from seven horses over 12 months demonstrated that season, changes in forage, and ambient weather conditions caused significant variations. [2]


The predominant types of bacteria present in the equine gastrointestinal microbiome are from the phyla (taxonomic rank) Firmicutes and Bacteriodetes. Many genera, species and strains of bacteria are classified under each of these two phyla.

The Firmicutes phylum includes the genera Lactobacillus and Streptococcus and accounts for 20-59% of the microbial population in the equine gut.

The Bacteroidetes phylum includes the genera Prevotella and Bacteroides and comprises 2-65% of the microbiome.

There is a significant difference between the composition of bacteria in the horse’s stomach and small intestine compared to the large intestine. [4]

We are experiencing an explosion of information regarding the horse’s gastrointestinal microbiome but there are diverging results both between studies and between horses within studies. We do know the microbes populating the stomach and small intestine are geared toward utilizing simple carbohydrates (sugars and starch) and protein while the fibre-fermenting microbes reside in the cecum and colon. [21]

Roles in Digestion

In horses, several bacteria are involved in digestion. Firmicutes and the Fibrobacteres phylum primarily digest cellulose while Bacteroidetes break down pectins and glycans as well as hemicellulose.

Yeast strains, such as Saccharomyces boulardii, and fungi also aid in digestion and nutrient assimilation.

Through microbial fermentation, the digestive process yields volatile fatty acids (VFAs), which are a source of energy used by the horse. [3]

Microorganisms in the gut are also involved in the synthesis of important nutrients including vitamin K and B vitamins such as folate.