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 of the gastrointestinal tract can occur if the microbial population becomes unbalanced or dominated by harmful microbes.
Horses with dysbiosis may develop excessive permeability of the intestinal barrier (sometimes referred to as Leaky Gut Syndrome), leading to ulcers or colitis and increasing the risk of laminitis.
Some of the most common causes of dysbiosis in horses include a diet that is high in rapidly fermented starches or sugars, exposure to stress, and use of medications or deworming drugs.
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 or other areas of the body.
Treatments for dysbiosis may include making changes to the diet of affected horses and replenishing the beneficial bacteria of the gastrointestinal system by using pre- and probiotics.
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 glucose metabolism in horses and humans.
The equine gastrointestinal system contains thousands of different species of bacteria, yeast, fungi, and protozoa. 
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. 
The predominant types of bacteria present in the equine gastrointestinal microbiome are from the phyla (taxonomic rank) Firmicutes and Bacteriodetes. Many species and strains of bacteria are classified under each of these two phyla.
The Firmicutes phylum includes the Lactobacillus and Streptococcus species and accounts for 20-59% of the microbial population in the equine gut.
The Bacteroidetes phylum includes the Prevotella species and comprise 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. 
A diverse range of bacteria inhabits the stomach and small intestine compared to the large intestine which hosts a more uniform range of bacteria.
Roles in Digestion
In horses, several bacteria are involved in digestion. Firmicutes and Fibrobacteres aid in the digestion of cellulose while Bacteriodes break down pectins and glycans such as hemicellulose.
Yeast species, 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. 
Microorganisms in the gut are also involved in the synthesis of important nutrients including vitamin K and B vitamins such as folate.
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, the condition is referred to as dysbiosis.
Dysbiosis can negatively impact overall health in many ways. It is associated with Leaky Gut Syndrome 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 promote the condition. 
Antibiotics are also a known cause of dysbiosis in horses.  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.
Excess 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 increase in Lactobacilli and Streptococci in the cecum and colon of ponies fed barley at 29 hours post-feeding. These changes occurred regardless of whether the diet contained 30% or 50% barley. 
Dysbiosis can result as a natural response when a horse becomes ill or is exposed to stress during competition or transport.
Symptoms of Dysbiosis in Horses
Horses with dysbiosis 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 of dysbiosis. Possible signs of dysbiosis may include:
- Weight loss
- Sore or stiff joints
- Poor exercise tolerance
- Breathing issues
- Changes in disposition
- Irritable bowel syndrome
- Inflammatory bowel disease
- Bacterial infections in the bowel
- Hypermotility (diarrhea)
- Systemic inflammation
Dysbiosis is also associated with a number of other conditions, including laminitis, metabolic dysfunction and dental issues.
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. These changes can cause diarrhea and promote infection within the gastrointestinal tract, leading to bowel damage and systemic inflammation.
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.
In horses with large intestinal colic, lactic acid bacteria Lachnospiraceae, and Lactobacillaceae were overgrown. 
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. 
Post-partum, the mares’ intestinal tracts had a reduction in typically dominant bacteria from the Firmicutes phylum which preceded colic episodes.
The influence of certain types of bacteria in the development of laminitis is unknown. However, a known cause of laminitis is the ingestion of lush grass and grain overload.
The relationship between the microbiota, metabolism and the endocrine system is highly complex.
According to one research study, horses diagnosed with Equine Metabolic Syndrome (EMS) exhibited differences in their microbiome when compared to healthy horses. 
A study of 24 horses determined modest changes in the gastric glandular mucosal microbiome in horses with EGGD. 
Imbalances in the gastrointestinal microbiome can affect the teeth. An imbalance in healthy and harmful bacteria may promote an immune response that increases inflammation in the mouth and teeth.
Diagnosis of Dysbiosis in Horses
Making a definitive diagnosis of dysbiosis may require the use of multiple testing strategies.
A fecal sample is valuable for assessing what types of microorganisms are present in the gastrointestinal tract of a horse suspected of having dysbiosis.
There is often a reduction in the diversity of organisms in the feces of horses with dysbiosis.
To determine the causative agent in a horse with dysbiosis, the feces may be assessed using a polymerase chain reaction (PCR) test, stool culture, or toxin screening method. Intestinal and rectal biopsies may also be taken.
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.
Evaluating horses for symptoms including changes in manure (from a solid to a loose or runny consistency), Free Fecal Water Syndrome, poor eating habits, and a loss of condition help to aid in a diagnosis.
A fecal occult blood test is a screening exam that can be used to diagnose blood loss in the foregut and or hindgut. This test uses antibodies to detect hemoglobin and albumin in an equine fecal sample to indicate blood loss.
Treatment of Dysbiosis in Horses
Left untreated, dysbiosis in horses can potentially lead to serious secondary medical complications. Potential complications resulting from dysbiosis include laminitis, founder, and insulin-related issues.
If you notice changes in your horse’s 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.
Because dysbiosis can cause excess fluid loss, affected horses should be kept well hydrated.
Adding electrolytes to water can help to encourage horses to drink and prevent dehydration. In horses with advanced dehydration, fluid replacement via intravenous administration may be necessary.
Probiotics & Prebiotics
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. 
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).
Research shows that Saccharomyces cerevisiae may protect the bacterial ecosystem in horses being transported and reduce the risk of dysbiosis. 
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.
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. 
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 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.
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