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.

Mad About Horses
Join Dr. Chris Mortensen, PhD on an exciting adventure into the story of the horse and learn how we can make the world a better place for all equines.
Apple Podcasts Spotify Youtube
Mad Barn - Equine Nutrition Consultants

What is Dysbiosis?

The microorganisms that normally inhabit the equine gastrointestinal tract exist in harmony and aid in the digestion process and assimilation of nutrients.

If the microbial population within the intestinal tract becomes unbalanced and dominated by harmful microbes associated with a disease state, the condition is referred to as dysbiosis.

Dysbiosis can negatively impact overall health in many ways. It can be associated with Leaky Gut or intestinal hyperpermeability in which the tight junctions between cells that line the intestinal wall become loose.

This can result in further complications including systemic inflammation and endotoxicosis, affecting the well-being of your horse.

What Causes Dysbiosis?

Several factors can influence the development of dysbiosis in horses.


Certain types of medication can promote dysbiosis. For example, the nonsteroidal anti-inflammatory drug (NSAID) phenylbutazone is known to cause gastrointestinal injury and impaired intestinal barrier function which can also be associated with dysbiosis. [5]

Antibiotics are also a known cause of dysbiosis in horses. [6] Antibiotics destroy the beneficial and harmful bacteria in the gastrointestinal system thus causing an imbalance in the microbiome. Antibiotic-induced colitis is a common type of dysbiosis.


Changes in diet are a frequent cause of dysbiosis in horses. Any time your horse is switched to a new hay source or feed, changes in the microbial population of the gut are likely to occur.

This is why it is recommended to make feed changes gradually to allow the microbiome to adjust.

Excessive consumption of grain that is high in rapidly fermented starches and sugars can decrease hindgut pH potentially causing hindgut acidosis and shifting microbial populations.

One study demonstrated an abrupt shift to the diet containing barley caused an increase in Lactobacilli and Streptococci in the cecum and colon of ponies. These changes occurred regardless of whether the diet contained 30% or 50% barley. [7]

However, these changes are to be expected because starches are fermented by different organisms than those which ferment fibre. These changes are not harmful unless acidosis is severe enough to damage the intestinal wall.


Dysbiosis can result as a natural response when a horse becomes ill or is exposed to stress during competition or transport. Exercise and heat stress can also induce alterations in the gut microbiome.


Using anthelmintic drugs to kill parasites in the gut can promote multiple significant changes in the digestive tract including alterations in microbial populations. [8] However, in most cases these changes are minor, short-lived and correct themselves.

Intestinal Parasites:

Conversely, intestinal parasitism has also been found to have an influence on the microbiome. [22][23]


Low dose dietary contamination with mycotoxins has been shown to cause dysbiosis in other species. [25][26] This should be a concern in the horse as well.

Symptoms of Dysbiosis in Horses

The microbial population in the horses GI tract is very adaptable and fluid. Not all changes are harmful. It is only when a disease state results, such as colitis or inflammatory bowel disease, that the term dysbiosis applies.

Horses with dysbiosis-related disorders may display a wide range of clinical symptoms depending on the area of the intestine affected and the microorganisms present or missing. Symptoms may also differ between chronic and acute cases.

Small intestine disorders that may involve dysbiosis can result in:

Signs of hindgut disease include:

  • Variable appetite
  • Bloating
  • Hypermotility (diarrhea)
  • Colic
  • Weight loss

Associated Conditions

At present, knowledge of the extent of the pathologic effect of an imbalanced microbiome on the various systems of the body is limited.

Further research is required to determine the association of the microbiome with the following conditions:


In cases of colitis, alterations in the microbial populations cause inflammation in the intestinal lining and cellular dysfunction. A common cause is chronic NSAID use.

These changes can cause diarrhea and promote infection within the gastrointestinal tract, leading to bowel damage and systemic inflammation.

Commonly involved organisms are Salmonella and pathogenic Clostridia.


One study demonstrated that horses with intestinal diseases had fewer microbial colonies in their gastrointestinal system and a less diverse microbial population compared to healthy horses. [9]

In horses with large intestinal colic, lactic acid bacteria Lachnospiraceae, and Lactobacillaceae were overgrown. However, the significance of these findings and whether they were cause or effect could not be determined. [9]

Dysbiosis is implicated in the development of gas-related colic and large colon torsions because of gas production by microbes.

The by-products of microbial metabolic processes may negatively influence intestinal motility.

Although research connecting microbial disturbances to colic is lacking, one study involving pregnant mares demonstrated a change in their microbiome as a potentially increased risk for the development of colic. [10]

Post-partum, the mares’ intestinal tracts had a reduction in typically dominant bacteria from the Firmicutes phylum which preceded colic episodes.


Feed room break-ins, where horses gorge themselves on grain, as well as experimental overloads with pure cornstarch or chickory root fructan, result in laminitis related to dysbiosis in the hind gut.

The overload of easily fermentable substrate leads to proliferation of Streptococci and damage to the intestinal lining which can allow bacteria and their toxins to enter blood. This triggers a systemic inflammatory response which can induce laminitis.

In addition, the bacterial enzymes such as thermolysin and bacterial endotoxins circulating in the blood activate matrix metalloproteinase enzymes which damage the laminae of the hoof. [11][24] These effects link carbohydrate overload-induced laminitis with laminitis caused by severe gut infections or colic.


Bacterial colonization and the resulting dysbiosis may contribute to spontaneous equine glandular gastric disease (EGGD). [13]

A study of 24 horses determined modest changes in the gastric glandular mucosal microbiome in horses with EGGD. [14]

Diagnosis of Conditions Related to Dysbiosis in Horses

Evaluating horses for symptoms including changes in manure (from a solid to a loose or runny consistency), poor eating habits, and a loss of condition can provide a diagnosis.

Although tests are available for examining the bacteria present in manure, we do not have sufficient knowledge to link any pattern of organisms to a specific disease state.

When a pathogenic organism is involved, it can be identified in feces using a polymerase chain reaction (PCR) test, stool culture, or toxin screening method. Intestinal and rectal biopsies may also be taken if inflammatory bowel disease is suspected. In addition, rectal examination and abdominal ultrasound can detect abnormal loops of bowel.

Blood tests including a complete blood count and chemistry panel may be helpful. Tests may provide information about biochemical abnormalities caused by the condition, the presence of additional illness, and infection due to viral, bacterial, and parasitic agents.

Treatment of Dysbiosis in Horses

Left untreated, dysbiosis in horses can potentially lead to serious secondary medical complications. Potential complications resulting from dysbiosis include inflammatory bowel disease, colitis, colic, and systemic inflammatory response-related laminitis.

If you notice changes in your horse’s appetite or manure, contact your veterinarian as soon as possible. Consulting a veterinarian to establish a plan for prompt treatment of the condition increases the prognosis for a successful recovery.

When dysbiosis is present, nutrient absorption is compromised and can lead to malnutrition. Supportive therapy is needed to restore the balance of flora residing in the equine gastrointestinal system.

Support Hydration

Because dysbiosis can cause excess fluid loss, affected horses should be kept well hydrated.

Adding plain salt or electrolytes to water or feed can help to encourage horses to drink and prevent dehydration. If these are added to water, always offer plain water as well. In horses with advanced dehydration, fluid replacement via intravenous administration may be necessary.

Probiotics & Prebiotics

A combination of probiotics and prebiotics should be administered to aid in recovery from dysbiosis.

Probiotics help to replenish beneficial bacteria that protect against toxins, combat pathogenic bacteria, stimulate immunity, and lower the pH of the gut to make it less hospitable to pathogens. [15]

Unlike probiotics which are living organisms, prebiotics are soluble plant fibres that cannot be digested by enzymes in the stomach or small intestine.

Prebiotics such as xylooligosaccharides (XOS), polydextrose, galactooligosaccharides (GOS), pectin, and psyllium provide a source of food for probiotics to thrive on.

In one study involving 29 neonatal Thoroughbreds with diarrhea, the duration of the condition was shorter in the probiotics-administered group (approximately 7+ days) compared to the control group (approximately 14 +/- 3 days).

These results indicate that beneficial microbes help regulate intestinal function and may prevent diarrhea. [19]

Yeast Cultures

Yeast is also beneficial for reducing the risk of dysbiosis and re-establishing and maintaining a healthy gastrointestinal tract. [16]

Research shows that Saccharomyces cerevisiae may protect the bacterial ecosystem in horses being transported and reduce the risk of dysbiosis. [7]

To help affected horses recover from dysbiosis, a reduction in the consumption of lush pasture or grain may be necessary to prevent acidosis in the hindgut. Probiotics may help to reduce the effects of high-grain diets on the gut microbiome.

Microbial Transplant

Fecal transfaunation or microbial transplant involves the transfer of healthy microbe sources from the feces of one horse to the digestive tract of another.

Transfaunation has been shown to significantly improve intestinal health in horses with dysbiosis by establishing a more diverse microbiome and restoring gut function. [18]

This strategy has been successfully used in some horses to treat chronic diarrhea caused by dysbiosis.

In horses with diarrhea, treatment with antibiotics or fecal transfaunation that resolves the problem provides reasonable evidence that dysbiosis was present.

How to Prevent Dysbiosis in Horses

If your horse is being treated with antibiotics, it may be helpful to administer a probiotic during and after treatment to prevent the growth of abnormal intestinal flora.

Similarly, administering a probiotic before and after deworming may help to guard against dysbiosis.

A diet consisting primarily of high-quality roughage is critical for maintaining a healthy microbiome. Diet changes should always be introduced over time to allow the flora within the gastrointestinal tract to adapt.

Some horses will require a minimal amount of grain in their diet to prevent dysbiosis. Using high-quality oils or energy dense, easily fermented fibre such as beet pulp or soy hulls may serve as an alternative energy source to grain for some horses.

Feeding and management practices can go a long way to preventing dysbiosis. Feeding a probiotic/prebiotic regularly is helpful for supporting the beneficial microbial populations in the digestive tract and reducing the risk of dysbiosis.

Optimum Digestive Health

5 stars
4 stars
3 stars
2 stars
1 star

Learn More

  • Prebiotics, probiotics & enzymes
  • Support hindgut development
  • Combats harmful toxins in feed
  • Complete GI tract coverage

Is Your Horse's Diet Missing Anything?

Identify gaps in your horse's nutrition program to optimize their well-being.


  1. Kauter, A. et al. The gut microbiome of horses: current research on equine enteral microbiota and future perspectives. J Vet Intern Med. 2019.
  2. Salem, SE et al. Variation in faecal microbiota in a group of horses managed at pasture over a 12-month period. Sci Rep. 2018.
  3. Bentz B. G. Digestion in the horse. The Horse. 2014.
  4. Ericsson, A. et al. A Microbiological Map of the Healthy Equine Gastrointestinal Tract. Plos One. 2016.
  5. Whitfield-Cargile, C. et al. Effects of phenylbutazone alone or in combination with a nutritional therapeutic on gastric ulcers, intestinal permeability, and fecal microbiota in horses. J Vet Intern Med. 2021.
  6. Costa, C. et al. Changes in the equine fecal microbiota associated with the use of systemic antimicrobial drugs. BMC Vet. 2015
  7. de Fombelle, A. et al. Feeding and microbial disorders in horses: 1-effects of an abrupt incorporation of two levels of barley in a hay diet on microbial profile and activities. J Equine Vet Sci. 2001.
  8. Kunz, I. et al. Equine Fecal Microbiota Changes Associated With Anthelmintic Administration. Journal of Equine Veterinary Science. 2019.
  9. Taemook, Park et al. Comparison of the Fecal Microbiota of Horses with Intestinal Disease and Their Healthy Counterparts. Vet Sci. 2021.
  10. Weese J.S. , Holcombe S.J., Embertons R.M., Kurtz K.A., Rossner H.A., Jalali M., Wismer S.E. Changes in the faecal microbiota of mares precede the development of post partum colic. Equine Vet. 2015.
  11. Kyaw-Tanner, M.T. et al. Equine laminitis: membrane type matrix metalloproteinase-1 (MMP-14) is involved in acute phase onset. Equine Vet J. 2008.
  12. Frank, N. et al. Equine metabolic syndrome. J. Vet. Intern. 2010.
  13. Banse HE et al. Equine glandular gastric disease: prevalence, impact and management strategies. Vet Med. 2019.
  14. Paul, L. et al. Gastric microbiome in horses with and without equine glandular gastric disease. Journal of Veterinary Internal Medicine. 2021.
  15. Schoster A. et al. Probiotic use in horses – what is the evidence for their clinical efficacy?J. Vet. Intern. Med. 2014.
  16. Elghandour, M.M.Y. et al. Saccharomyces cerevisiae as a probiotic feed additive tonon and pseudo-ruminant feeding: a review. J Appl Microbio. 2019.
  17. Faubladier C. et al. Effect of transportation on fecal bacterial communities and fermentative activities in horses: Impact of Saccharomyces cerevisiae CNCM I-1077 supplementation. J. Anim. Sci. 2013.
  18. McKinney, C. et al. The fecal microbiota of healthy donor horses and geriatric recipients undergoing fecal microbial transplantation for the treatment of diarrhea. Plos One. 2020.
  19. Tanabe, S. et al. Anti-inflammatory and Intestinal Barrier-protective Activities of Commensal Lactobacilli and Bifidobacteria in Thoroughbreds: Role of Probiotics in Diarrhea Prevention in Neonatal Thoroughbreds. J Equine Sci. 2014.
  20. Ahmad, R. et al. Loss of claudin-3 expression increases colitis risk by promoting Gut Dysbiosis. Gut Microbes. 2023.
  21. Chaucheyras-Durand, F. et al. Gastro-Intestinal Microbiota in Equines and Its Role in Health and Disease: The Black Box Opens. Microorganisms. 2022.
  22. Peachey, L.E. et al. The relationships between faecal egg counts and gut microbial composition in UK Thoroughbreds infected by cyathostomins. Int J Parasitol. 2018.
  23. Peachey, L.E. et al. Dysbiosis associated with acute helminth infections in herbivorous youngstock – observations and implications. Sci Rep. 2019.
  24. Mungall, B.A. and Pollitt, C.C. Thermolysin activates equine lamellar hoof matrix metalloproteinases. J Comp Pathol. 2002.
  25. Djouina, M. et al. Low dose dietary contamination with deoxynivalenol mycotoxin exacerbates enteritis and colorectal cancer in mice. Sci Total Environ. 2023.
  26. Shanmugasundaram, R. et al. Subclinical doses of dietary fumonisins and deoxynivalenol cause cecal microbiota dysbiosis in broiler chickens challenged with Clostridium perfringens. Front Microbiol. 2023.