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Dysbiosis & the Microbiota in Horse Health & Disease

Dysbiosis refers to a profound imbalance in the intestinal microbiota which precipitates changes in the normal health and function of the gastrointestinal tract. In horses, this may manifest in colitis, laminitis and colic and other clinical situations. Additionally, recent research findings indicate that more subtle changes in the microbial population of the horse are even more common and can have health implications. With that, the intestinal microbiota is undergoing a renewed surge in interest, in both veterinary and human research, as links are being found with the immune system, the neurologic system and glucose metabolism.

Equine veterinary medicine has long understood the importance of the microbiota on the health of the horse, in digestion of the fibrous diet, and the impact of derangements to the microbiota causing diseases such as colitis and laminitis. Now, links to diseases such as Equine Metabolic Syndrome are also being investigated.

Background on Equine Microbiota and Health

The equine intestinal microbiome is composed of bacteria, archaea and eukarya (protozoa and fungi). This composition is influenced by factors such as host genetics, diet, environment and changes to gut homeostasis (Martin et al, 2017).

In horses, the microbiome is essential for digestion of the fibrous diet. Many of the bacteria involved in this process are uncharacterized, however the Firmicutes and Fibrobacteres species are known to use cellulases to degrade cellulose, while the Bacteroides species (e.g. Prevotella) can degrade pectins and use saccharolytic processes to break down glycans such as hemicellulose.

This process results in the production of volatile fatty acids (VFAs), which are then converted to energy sources. The microbiome is also responsible for producing some vitamins for the horse, especially vitamin K, and some B vitamins like folate.

Evidence is emerging that the microbiota is involved in more than just food digestion. In fact, the microbiome, and various metabolic by-products of the organisms themselves, interact with the immune system as well, and also participate in various aspects of normal metabolism, such as the Tricarboxylic acid cycle, bile acid recycling, and the glucose-insulin feedback loop.

Large-scale disturbances of the intestinal microbiota (dysbiosis) of the horse is known to occur after a sudden change of diet, and is particularly obvious after grain overload, but smaller-scale disturbances also likely occur with smaller changes to diet and resulting from diets rich in complex carbohydrates such as grain.

Antibiotic-induced colitis is also a well-recognized form of dysbiosis.

In research on the mouse model, researchers have found a link between the maternal microbiota (specifically certain bacteria) and abnormal brain development of the fetus, driven by the maternal immune system.

This finding underpins the likely importance of the intestinal microbiota, in health and disease, for all mammalian species.

Emerging Research into Equine Microbiota

In horses the following research is underway:

  • Classification of the Equine Microbiome e.g. the Equine Microbiome Project.
  • The effect of diet on the microbiome, and the impact on the long-term health of the horse.
  • How the microbiome changes as foals grow into adults and what are the influential factors on this.
  • How do stressors such as training, travel, foaling, anesthesia and surgery affect the microbiome?
  • How do antimicrobials and anthelminthics affect the microbiome?

The results of this research are not definitive yet, but what is known is that there is a large amount of individual variation in the equine microbiota and that a “standard” microbiota may not exist. However, there are some general patterns, in that Firmicutes and Bacteroides species make up the bulk of the microbiota, but their percentages vary considerably. See Table 1.

Table 1

Classification of bacteria genera identified in the horse hindgut using sequencing techniques (from Julliand et al, 2016).

ClostridaceaeClostridium Sarcina
LachnospiraceaeButyrivibrio and Pseudobutyrivibrio
RuminococcaceaeRuminococcus and Sporobacter>/i>
VeillonellaceaeMegasphaera, Mitsuokella and Veillonella
Beta-proteobacteriaBurkholderialesAlcaligenaceae and Oxalobacteraceae
MycoplamatalesIncertae sedis

Pathophysiology of the Equine Microbiome and Disease Relationship

To date, we only know a small amount about the extent of the pathologic effect of an imbalanced microbiota.


Changes to the intestinal microbiota cause inflammation of the intestinal mucosa and dysfunction of the cells, which could lead to diarrhea, damage to the bowel and systemic inflammation and infection.

The bacterial species Lachnospiraceae and Ruminococcaceae (phylum Firmicutes) have been associated with intestinal health in other mammalian species, and have been found to be significantly lower in abundance in horses with diarrhea.

Actinobacteria and Spirochetes species have also been found to decrease in horses with idiopathic colitis, while Fusobacteria species increase.

The role these bacteria play, along with the better known causes of colitis such as Salmonella and Clostridium difficile are yet unknown.


The microbiota produce gas, as a side effect of their metabolic processes, and this is likely to have an impact on the development of gas-related colics, including large colon torsions. Intestinal motility may also be affected by the by-products of microbial metabolic process.

Few studies have yet shown a direct link between certain microbial disturbances and colic; however, in a study on pregnant mares, it was found that when a change in the microbiota was detected the mare was significantly more likely to develop colic (Weese et al. 2015). In the study, Weese and team say, “Associations between Firmicutes (particularly Lachnospiraceae and Ruminococcaceae) and Proteobacteria and development of colic could lead to measures to predict and prevent colic (in post-partum mares).”


Laminitis has long been associated with dietary changes, such as ingestion of lush grass and grain-overload. The interplay between dysbiosis, intestinal inflammation and the development of laminitis are well studied, however the precise details of whether certain strains of bacteria have a bigger influence are yet unknown.

Gastric Ulcer Disease

Since Helicobacter bacteria were discovered to be involved in the pathology of gastric ulcers in humans, a microbial influence has been suspected in horses. The role of bacteria and how the diet can cause or prevent gastric ulceration is an area of ongoing research.

Equine Metabolic Syndrome (EMS)

The link between obesity, disorders of glucose-regulation and the microbiota is being intensively researched in humans, and has led to similar investigations in horses with EMS. One study so far has found that horses with EMS have decreased microbial diversity. The interplay between the microbiota and the host metabolism and endocrine system is highly complex.

Clinical Presentation of Dysbiosis in Horses

The clinical signs of dysbiosis are diverse and depend on the area of intestine affected and the acute or chronic nature of the disruption to the microbiota, as well as which bacteria play a prominent role (or fail to play a protective role).

Known clinical signs of dysbiosis:

Systematic InflamationMucous membrane congestion or toxic changes
Fever, etc.

Clinical signs that potentially could be related to dysbiosis:

Diagnosing Dysbiosis in Horses

Definitively diagnosing dysbiosis at this point in time not easy.

With colitis, a causative agent might be identified through culture or PCR on fecal samples or intestinal biopsies and screening for toxins in the feces.

In cases of diarrhea, a positive clinical response to treatment either with an antibiotic or transfaunation of intestinal contents/feces from a healthy horse might provide a strong suspicion of dysbiosis as the cause.

For all of the other diseases, where the precise association of the microbiota with the disease is not known, a diagnosis at this point in time is not possible – however this is likely to change in the future.

Tests that help identified dysbiosis, and its side effects such as intestinal inflammation and intestinal disease, may include:

  • A fecal occult blood test such as the SUCCEED Fecal Blood Test, which is a stall side screening test utilized by veterinarians to detect antibodies to hemoglobin and albumin in an equine fecal sample. This test assists in diagnosing foregut, hindgut, or simultaneous foregut and hindgut blood loss.
  • Biopsy of the intestine or rectum
  • PCR panels to screen for:
    • Any obvious change to the microbial profile (these profiles are not currently readily available)
    • The presence of pathological agents (bacterial, viral, helminthic)

Treatment for Dysbiosis in Horses

The treatment of dysbiosis may be complex as there could be some innate/genetic variations in how the host interacts with the microbiota that drives the overall microbial profile for the individual horse.

Probiotics, or “good” live microorganisms, have not yet been shown to have significant benefits. However, fecal transfaunation has been shown to significantly improve intestinal health, for example in horses with chronic diarrhea.

Prebiotics provide a nutrient source for microorganisms in the gut and thus may be helpful in encouraging the growth of beneficial bacteria. Prebiotics can include fructooligosaccharides (FOS), xylooligosaccharides (XOS), polydextrose, mannon oligosaccharides (MOS), galactooligosaccharides (GOS), pectin and psyllium.

Preventing Dysbiosis in Horses

Maintaining a healthy intestinal function is likely crucial to prevention of dysbiosis.

A diet predominantly composed of high quality roughage is important, and diet changes should always be made slowly. In horse breeds that evolved on poorer quality diets, or are otherwise prone to problems with lush green grass, feed a predominantly hay diet.

Minimize the amount of grain fed to the horses, and where possible, supplement with high quality oils as an alternative energy source.


  • Julliand, V. and Grimm, P. (2016) Horse Species Symposium: The microbiome of the horse hindgut: History and current knowledge. Journal of Animal Science.
  • Martin, E.J. et al (2017) Normal variation and changes over time in the equine intestinal microbiome. Abstract. Journal of Equine Veterinary Science, 52, p 60.
  • Weese, S. (2017) Role of the Equine Microbiota in Health and Disease. ACVIM conference proceedings.
  • Weese, J. S., Holcombe, S. J., Embertson, R. M., Kurtz, K. A., Roessner, H. A., Jalali, M., & Wismer, S. E. (2015). Changes in the faecal microbiota of mares precede the development of post partum colic. Equine veterinary journal, 47(6), 641-649.

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