The Equine Microbiome: Diet, Disease, and Behaviour

Written by Holly Heartz, MSESS, RD

Bright pink bacteria under an electron microscope. Cover image.

Summary: Gut bacteria play an important role in digestion and overall health in horses, including their behavioral health. This article introduces the equine gut microbiome and explores how changing a horses’ diet could influence their welfare through encouraging a change in microbiota composition.

Over the past 25 years as a registered dietitian, I have witnessed an increase in knowledge regarding intestinal health and management of disease with nutrition. This is possible in all mammalian species. Recently, there is a focus on fixing gut function for those with digestive issues and improving gut-brain communication for those dealing with anxiety and depression. Food can influence gut and mental health. Using nutrition strategies often works better than medication to improve mental health. Extensive research is being conducted on the gut microbiome, which is key to improving gut and brain health.

In the equine, digestion in the foregut is like most other mammals. However, the hindgut (the cecum and colon) differs in terms of where the complex environment of microbiota resides. Here, both beneficial and harmful organisms reside, and their composition fluctuates, even in healthy horses.1

Introducing the microbiota

Internally, an array of various microbes resides along the gastrointestinal tract (GIT) from mouth to rectum. Microbes in the upper GIT (stomach, ilium, and jejunum) are variable, with the most predominant phylum being proteobacteria. Proteobacteria play a role in nitrogen fixation, a process necessary for the biosynthesis of amino acids.2

Most interest is focused on the hindgut. Organisms here are mainly bacteria (see sidebar) with the main players being Bacteroidetes, Firmicutes, and Verrucomicrobia. 2

These microbes produce short chain fatty acids (SCFAs), also known as volatile fatty acids, specifically acetate, propionate, and butyrate. These metabolites benefit health and wellbeing by maintaining the integrity of the mucin layer and decreasing bowel inflammation, promoting immunity, and reducing disease and pathogen risk.1,2

Firmicutes produce butyrate, which is an energy substrate for colonocytes and is vital in maintaining gut health.2,3 Acetate and propionate are transported to the liver and metabolized. Propionate is a substrate for gluconeogenesis (the process of producing blood glucose). Acetate is a significant fuel in peripheral tissues.3

The function of microbiota in the gut

Eating initiates the process of activating the gut microbiome. For the horse, chewing the forage and feedstuff breaks it down into smaller pieces. This increases the surface area to allow the microbes greater access to the food. Chewing also stimulates saliva to moisten the food. In contrast to humans, horses do not produce much of the digestive enzyme amylase, which starts carbohydrate digestion, in the mouth. Food is churned in the stomach, which aids its passage to the small intestines. In the small intestines, amino acids and fats are absorbed and there is some carbohydrate digestion. Water and electrolytes are transported to the large intestines, which is the major site of digestion in the horse.3

Fibrous foodstuffs cannot be digested without the gut microbiome. The microbes break down the cell walls of plant material through fermentation and produce SCFAs. This process regulates fatty acid composition, supplies essential nutrients, and improves the bioavailable of energy consumed by up to 70%.1,4,5

SCFAs are a major player in the maintenance of gut and immune homeostasis. Their signaling mechanism influences host physiological processes such as chemotaxis and phagocytosis, as well as inducing reactive oxygen species. They can change cell proliferation and function, help regulate metabolism, alter gut integrity, and have anti-inflammatory, antitumorigenic, and antimicrobial effects.6

The good and bad: health and disease

Each individual horse’s microbiome is unique. The composition of the microbiome is an accumulation of everything the horse has encountered and consumed during its life and is continually being modified by endogenous and exogenous factors.

The promotion of more beneficial bacteria improves the horse’s wellbeing. There is a strong relationship between the composition of the gut microbiome and health and disease prevention. In humans, housing more beneficial bacteria is important, as once an organism occupies a space in the gut, it is difficult to bring another organism into that same space. However, the equine digestive system and its microbiome are more sensitive to change: A change in their environment, dietary changes, exposure to pathogens, ingestion of certain medications, and even pregnancy can alter the microbiome for the worse.2

The microbiome is vulnerable to infection, and some bacteria induce inflammation. For example, infection by Neorickettsia risticii can lead to Potomac horse fever.2 Certain drugs only work if the right microbes are present to activate those drugs. Other microbes degrade drugs. Excessive use of antibiotics is associated with bacterial overgrowth, and antimicrobials can change microbiome composition, leading to colitis. An abnormal increase in bacteria that do not normally reside in the small intestine (termed small intestinal bacterial overgrowth or SIBO in humans) can result from antibiotic use and lead to colic. Inflammatory intestinal disease and dysbiosis can occur from normal resident bacteria, proteobacteria, in the small intestine when it becomes overabundant .2

An appropriate balanced diet is necessary to promote a strong microbiome. In humans, bacterial diversity in the gut is linked to better metabolic and GI health with improved digestion and nutrient absorption. Obesity, metabolic disorders, and many diseases are inflammatory processes. Individuals with lower microbial richness (decreased number of gut microbial genes), may have a higher incidence of adiposity, insulin resistance, and dyslipidemia than those with microbial richness.3 In domesticated horses, the diversity of the microbiome is lower than in non-domesticated horses. The social structure differences inflicted on domesticated horses may be one factor leading to this difference. A lack of microbiome diversity has been speculated as a reason for the sensitivity of horses to GI diseases.2

There are differences in gut microbiome between lean and obese humans, with more Firmicutes in obese individuals. With weight loss, there can be changes in the gut microbiome composition, diversity, and fecal SCFAs.3,4 Verrucomicrobia is also gaining attention in obesity and metabolic disease research in humans.2 There is little doubt that altering diet regimes for equines’ weight loss will also affect their gut microbiome.

A word about feces

The microbiota in the hindgut is constantly changing. The composition and fluctuation of microbiota are evident in fecal samples.1 Fecal samples represent microbes in the terminal part of the colon and do not accurately indicate all the microbes living in the cecum and colon. A colonoscopy sample would provide a better idea of the resident microbiome in the hindgut. Microbes and their abundance in relation to one another in the feces can be identified using a DNA sequencing technique. This DNA identification process provides a more efficient, more complete analysis of the present microbes’ communities than previous methods. Therefore, a better sense of microbe activity and the role of active genes will provide information on the connection between health and disease.

Establishing the microbiome

Age is an influencing factor in the microbes established within the microbiome. The initial microbiome depends on the location of birth and method of feeding. A richer, more diverse microbiome is established with vaginal birth and nursing. Just like human newborns, foals have a high proportion of proteobacteria. Due to limited immune protection, these bacteria rapidly multiply. With colostrum, more immune-enhancing microbes are introduced into the gut. By 7 days of age, Firmicutes are the main organisms, just as in humans. Coprophagia, a normal part of the foal’s development, will provide additional microbes from ingested manure from their dams. Interestingly, foals do not ingest manure from other mares.7 As the foal starts eating solid food, Bacteroidetesincreases.8 By 60 days of age, the microbiome population is relatively stable. Having a less rich microbiome composition established subjects the foal to diarrhea. Stool samples from foals with diarrhea show an increase in Enterobacteriaceae (e.g., Salmonella and E. coli).2

Gut microbiota can be altered with management practices such as shared environments and nutrition; medications (e.g., antimicrobials); diseases such as undifferentiated colitis, grass sickness, postpartum colic, acute and chronic laminitis, simple obstruction colic; diet change and supplementation of the individual; and age. By adulthood, the microbiota is well established. As horses age (19 to 28 years of age) their microbiomes show a decreased level with respect to the diversity of residing organisms.2


Microbiota composition within the gut influence many physiological processes including gut-brain communication, brain development and function, cognition, and behaviour.1,2 The microbiome affects the brain in what is termed the gut-brain axis. These processes are well documented in human and other mammalian studies. Stress, both physical and mental, can result in a modified and less diverse microbiota.1,9 Stressors such as early and abrupt weaning, infrequent feeding, and isolation influence the gut microbiome.1,2 A healthy microbiome can modulate the stress response, alter brain chemistry, and normalize behavior (like anxiety and depression).

Research by Santos et al. (2011)5 and Destrez et al. (2015)10 identified that high starch/low fibre diets alter the microbial composition and increase the risk of aggressiveness and stereotypic behaviours, particularly oral stereotypies such as crib-biting.1,10 Crib-biting is associated with increased levels of ghrelin, a hormone that regulates hunger and gut motility, as well as anxiety, stress, and fear-like behaviors via gut-brain axis signaling. This connection is evident in how stereotypies, hypervigilance, and aggressiveness result from stress hormones and the beneficial modification of gut microbiota.1

High physical exertion is another stressor, especially in conjunction with other factors experienced by an athlete. Elite athletes tend to train many days a week, often with limited rest, potentially leading to muscle damage. Food intake changes with more concentrates or suboptimal intake; traveling long distances, a change in living environment, unfamiliar people and horses, and competing are associated with elevated physical and emotional stress.

Being in these stressful situations, plus the addition of physical exertion, will affect the horse’s sensitive intestinal tract. Stress not only activates the central nervous system (CNS) but also the autonomic nervous system (ANS). The stimulated CNS releases catecholamines (norepinephrine [NE] and epinephrine) and glucocorticoids into circulation. The ANS releases NE and other neurotransmitters into the GI tract. NE has been shown to be a trigger for the overgrowth of some harmful microbes. Some microbes can more easily adhere to the intestinal wall or have enhanced virulence that compromises the integrity of the intestinal lining to promote inflammation and disease.1,2 The intestinal lining can become more permeable, subjecting the horse to microbial toxins and pathogens that leak through the tight junctions. For instance, there is a strong relationship between carbohydrate overload, endotoxemia (acid-producing bacteria leaking into circulation), and laminitis.2


While poor management practices are a cause of behaviour problems, feeding practice also requires consideration to influence the gut microbiome and behaviour.

The gut can become chronically inflamed if a high starch diet is continually fed. Destrez et al. (2015) tested the effect of a 57% hay (fibre) and 43% barley diet (starch).10 This diet disrupted the composition and activity of the large intestine ecosystem with an increase of anaerobic and lactate-utilizing bacteria, and an increase in granulocytes (an indication of inflammation). This effect remained for 10 days. Santos et al. (2011) reported that the SCFA composition increases with a high fibre diet.5 Excess starch ingestion can increase lactate-producing microbes, having implications for laminitis.9 Elevated plasma of the SCFA acetate was found to be greater for hay-fed compared to grain-hay-fed animals.3

A high-fibre, low-starch diet can be a major and easily modifiable factor in improving gut microbiota. Doing so will improve horse welfare by reducing disease states and helping the horses accommodate to stressful situations.9 Higher-fibre diets increase chewing time, thereby reducing the horses’ susceptibility to oral stereotypies.

Feeding the gut

Prebiotics provide the nutrients and energy needed by gut microbes. All fibre/forage in a horse’s diet, whether grass, timothy, or alfalfa, acts as a prebiotic. Oats, legumes, soy hulls, and beet pulp are also prebiotics. The choice of what type of forage to feed depends on the horse’s macronutrient and nutritional requirements considering its age, physical activity level, physiological status, and health. An equine nutritionist would be the ideal professional to guide you on the best forage to select for your horse.

Many commercial feeds are supplemented with probiotics, yeast, or extra amino acids, so if you use such products, you may already be giving your horse a digestive aidPurina Platinum Evolution Sport Elite is one such feed that contains probiotics, prebiotics, and yeast.

There are also products that can be added to a horse’s feed such as Purina’s ActivAge. This product is specific to senior horses and contains prebiotics.


Probiotics are said to be one way to heal the gut. Due to their popularity, one might think they are always helpful. While they do provide good gut bacteria, in humans regular use is associated with slower digestion and brain fog. Some may even be harmful and cause diarrhea. To work properly, probiotics need to reach the large colon and become established.

The addition of probiotics may be beneficial in normalizing behaviour as they have been shown to reduce anxiety and depression in other species. Evidence for probiotic use in horses is not strong and more research is needed into the horse’s hindgut microbial activity.2

Fecal Microbiota Transplantation (FMT)

In severe cases, FMT may be necessary to heal the gut by manipulating the gut microbiome. Consumers can purchase FMT products marketed to restore gut microbes; however, microbiome transfer via fecal transplant is more successful in disease states. FMT is used in humans with diarrhea and inflammatory bowel disease and may be a useful treatment in horses. The microbiome can be severely damaged with antibiotic treatment, and FMT can almost replenish the microbiome.7

In my practice

When I see horses for behavior problems I always ask about their diet. My main recommendation is to get the hay analyzed, as this is usually never done. Likely, people don’t know what to do with this information, so I provide direction (such as online feed calculators) if they want to ensure proper nutrient provision.

In disease states, such as laminitis, recommendations can be geared to some general adjustments based on current intake. Laminitis disturbs hindgut microbiota and their metabolites, so we would want to correct this as much as possible.

I saw one such laminitic horse who was obese. This gelding was 20 years old and likely obese most of his life (according to his owner). He was free-fed hay and had minimal pasture access daily. He was provided with Purina Evolution Elite in an amount to maintain body weight.

For weight loss, I recommended 1% of his body weight of soaked or steamed hay to reduce his sugar load. He was also removed from pasture, which would have too many fructans. We changed his feed to a lower-sugar, higher-fibre product – Supra Fibra Ultra. It contains yeast cultures that improve fermentation, help with hindgut pH, and improve the microbial population. We decreased the amount provided slightly from the amount for weight maintenance.

I’m skeptical of probiotics for horses. There is not much research on their effectiveness, they do not always produce beneficial results, and it could be a waste of money. Food is always first. I want to see if diet recommendations provide any benefit before any supplement is used.

While we often hope for drastic weight loss, a slower weight loss is preferred. This horse lost about 25 pounds in 6 months. If I had seen too fast of a weight loss, or he was stressed by the reduction in forage, I would have recommended increasing forage. I don’t want the horse’s metabolic rate to be reduced. Fat cells will multiply with an increase in body fat which makes fat loss more difficult.

This horse is no longer in a laminitic flare-up but he is still at risk. Since he is pain free and was not active previously, he can further increase his metabolism with exercise. It is not known what the horse’s microbiome was and is after the dietary intervention; however, change likely occurred.


While progressing rapidly, research on the GI microbiome is in its infancy for both human and veterinary medicine. Progress with horse health and disease prevention is lacking due to knowledge gaps. Research is needed to identify the key bacteria in the horse’s GIT and how best to deliver these bacteria, whether through the use of probiotics, FMT, or other interventions such as a purified stool substitute from a healthy donor.7 Before such interventions can be implemented, it is important to determine the core gut microbiota required for equines. We know of some of the main players but so much more needs investigation.


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  2. Kauter, A., Epping, L., Semmler, T., Antao, E-M., Kannapin, D., Stoeckle, S.D., Gehlen, H., Lübke-Becker, A., Günther, S., Wieler, L.H., & Walther, B. (2019). The gut microbiome of horses: Current research on equine enteral microbiota and future perspectives. Animal Microbiome 1(1):14.
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  5. Santos, A.S., Rodrigues, M.A.M., Bessa, R.J.B., Fereira, L.M., & Martin-Rosset, W. (2011). Understanding the equine cecum-colon ecosystem: current knowledge and future perspectives. Animal, 5:1, pp 48–56.
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  7. Mullen, K.R., Yasuda, K., Divers, T.J., Weese, J. S. (2018). Equine fecal microbiota transplant: Current knowledge, proposed guidelines, and future directions. Equine Veterinary Education, 30(3): 151–160.
  8. De La Torre, U., Henderson, J.D., Furtado, K.L., Pedroja, M., O’Malley, E., Mora, A., Pechanec, M.Y., Maga, E.A., Mienaltowski, M.J. (2019). Utilizing the fecal microbiota to understand foal gut transitions from birth to weaning. PLoS ONE14(4):e0216211.
  9. Destrez, A., Grimm, P., & Julliand, V. (2019). Dietary-induced modulation of the hindgut microbiota is related to behavioral responses during stressful events in horses. Physiology & Behavior, 202, 94–100.
  10. Destrez, A., Grimm, P., Cézilly, F., & Julliand, V. (2015). Changes in the hindgut microbiota due to a high-starch diet can be associated with behavioral stress responses in horses. Physiology & Behavior, 149, 159-164 

Holly Heartz, MSESS, RN, is a Registered Dietitian and Sports Nutritionist based in Fredericton, NB. She has been counselling athletes from recreational to Olympic since 1998. She applies practical advice based on sound scientific principles to help people understand nutrition. Her background is in exercise physiology and sport science, medical nutrition therapy, along with sport specific nutrition recommendations helps athletes attain their goals. She has also worked extensively with horses; her horse behavior and training services can be found here.

TO CITE: Heartz, H. (2022). The equine microbiome: Diet, disease, and behaviour. The IAABC Foundation Journal 25, doi: 10.55736/iaabcfj25.7