What You Need to Know About Your Horse’s Gut Microbiome

Understanding the equine gut microbiome can help you create and support healthy microbial populations in your horse’s digestive system.

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gut microbiome
The gut microbiome is an important factor in the overall health of the horse’s digestive system. | Getty images
The equine microbiome is a complex community of microbial populations found within every part of the digestive system, including the stomach and small intestine (foregut) and the cecum and large intestine (hindgut). The type and function of the microbiota present change from one segment to the next, and these different populations must work in harmony to maintain homeostasis and reduce the horse’s risk of disease and disorders.

The microbiota in the stomach and first sections of the small intestine function to break down starches, soluble sugars, readily fermented fibers, and proteins. The quantity of microbes varies depending on the type of diet, management factors, stress, and host variables. The latter parts of the small intestine show a gradual transition to the microbiota found in the hindgut. These microbes help ferment and break down the more complex fibers of the diet, including cellulose. Populations found in the cecum are similar to those in the first part of the large colon, but some changes do occur after the pelvic flexure (the hairpin turn where the cecum and colon come together).

Ideally, the equine microbiome would be the same across all horses, with the only variation being due to location within the digestive system. However, although some microbes reside in nearly all horses (a core population), the relative amounts of each can vary, and each horse’s microbiome is unique. The biggest variations are caused by seasonal effects on forage type and quality, dietary changes, different management styles, age, pathogen infections, and antibiotic treatments. The use of antimicrobials to treat disease can also negatively affect the microbial population because most will not differentiate between “bad” and “good” microbes. Some study results indicate it takes about a month for the microbial composition to return to normal after discontinuing antimicrobial administration.

The horse’s microbial population changes with age. A newborn foal has a very diverse population, likely acquired ex utero and from interactions with the dam. Some microbes will be transferred to the foal through the colostrum and milk. The foal also acquires microorganisms from the act of coprophagy (eating manure), usually at 3 to 5-days-old. Around one week of age, another change in the microbial population occurs, as the foal begins to experiment with solid food. As the foal ages, the population stabilizes, with changes only occurring during times of stress, such as alterations in diet, workload, and environment.

What Does the Microbiome Affect?

Recent studies have focused on the “microbiome-gut-brain axis” (MGBA) and how disruption of it can negatively affect behavior. Diets higher in starch and rapidly digestible and fermentable fibers can upset the balance of microbes and create a more acidic environment. Connections between the nervous, immune, and neuroendocrine systems might be affected, leading to undesirable behaviors such as reactivity, nervousness, aggression, and stereotypies.

The microbial population can affect the horse’s mental and physical health. Negative changes can lead to a variety of diseases and disorders, including gastric ulcers, diarrhea, colic, colitis, and laminitis. It can also have a negative effect on immune function, leading to increased susceptibility to infectious diseases.

How To Maintain a Healthy Microbiome

A healthy collection of microorganisms is vital for proper degradation of cellulose and hemicellulose in the hindgut, which provides more than 50% of the average horse’s daily energy requirements, as well as other vital nutrients. When this population is disturbed, colic and other metabolic disorders can occur, so always make changes to the horse’s diet gradually, usually over about two weeks. Pay particular attention to carbohydrates, fat, and protein. You can provide supplements designed to support a healthy microbiome, such as prebiotics, probiotics, and a relatively new product called postbiotics, to help prevent disorders related to digestive disturbances.

Management should focus on trying to minimize stress. Turnout is beneficial, and occasional “let-down” periods on pasture have been shown to improve the horse’s microbiome. Make sure adequate forage or higher fiber feedstuffs are available. Monitor horses for any signs of stereotypies (usually an early sign of stress or poor welfare), and monitor feed intake and aggressive behaviors. A decrease in feed intake and an increase in aggressive behaviors have been observed in horses with digestive disturbances.

Take-Home Message

Horse owners should always be aware of their horses’ digestive health and recognize issues that might indicate problems with the equine microbiota. Digestive system issues such as gastric ulcers, diarrhea, colic, and colitis and diseases such as laminitis and equine metabolic syndrome often indicate a disturbance in the gut microbiome. Avoid rapid dietary changes, especially in starch, fiber, and fat content. Although some contributing factors to issues with the microbiota, such as age and breed, can’t be changed by management, others, such as stress related to competition, transportation, and exercise, should be minimized as much as possible.


Adams VJ, LeBlanc N, Penell J. Results of a Clinical Trial Showing Changes to the Faecal Microbiome in Racing Thoroughbreds after Feeding a Nutritional Supplement. Vet Sci. 2022 Dec 30;10(1):27. doi: 10.3390/vetsci10010027. PMID: 36669028; PMCID: PMC9861731.

Chaucheyras-Durand F, Sacy A, Karges K, Apper E. Gastro-Intestinal Microbiota in Equines and Its Role in Health and Disease: The Black Box Opens. Microorganisms. 2022 Dec 19;10(12):2517. doi: 10.3390/microorganisms10122517. PMID: 36557769; PMCID: PMC9783266.

Kauter A, Epping L, Semmler T, Antao EM, Kannapin D, Stoeckle SD, Gehlen H, Lübke-Becker A, Günther S, Wieler LH, Walther B. The gut microbiome of horses: current research on equine enteral microbiota and future perspectives. Anim Microbiome. 2019 Nov 13;1(1):14. doi: 10.1186/s42523-019-0013-3. PMID: 33499951; PMCID: PMC7807895.

Mach N, Lansade L, Bars-Cortina D, Dhorne-Pollet S, Foury A, Moisan MP, Ruet A. Gut microbiota resilience in horse athletes following holidays out to pasture. Sci Rep. 2021 Mar 3;11(1):5007. doi: 10.1038/s41598-021-84497-y. PMID: 33658551; PMCID: PMC7930273.


Written by:

Janice L. Holland, PhD, is an Associate Professor and Director of Equine Studies at Wilson College in Chambersburg, Pennsylvania. A graduate of both Penn State and Virginia Tech, her equine interests include nutrition and behavior, as well as amateur photography. When not involved in horse activities she enjoys spending time outdoors enjoying nature.

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