The Equine Gut Microbiome and Its Role in Immunity and Behavior

By: Dr. Liz Schatz | Updated April 14, 2025

Your horse’s health may feel like a complicated puzzle you’re constantly trying to piece together. One day, they’re thriving, and the next, they’re struggling with digestive issues, unexplained weight changes, or a dull coat. While diet, exercise, and veterinary care all play a role, one of the most critical, yet under-researched, factors is the gut microbiome — a vast community of microorganisms that influence digestion, immunity, and even behavior. With nearly 70% of a horse’s immune system residing in the gut, understanding this microscopic world is key to ensuring long-term health.

Anatomy of the Equine Digestive System

Horses are hindgut fermenters, meaning microbial fermentation (when beneficial bacteria breaks down food to produce energy and nutrients) in the large intestine is essential for digestion. The digestive system consists of two main sections, each playing a vital role:

Foregut: Digestion and Nutrient Breakdown

The equine foregut is responsible for breaking down sugars, starches, proteins, and easily fermented fiber. Parts of the foregut include the:

• Mouth: Begins mechanical and enzymatic digestion.
• Esophagus: Transports food to the stomach.
• Stomach: Produces acid to break down food.
• Small Intestine: Absorbs nutrients, including proteins, fats, and simple carbohydrates.

Hindgut: Microbial Fermentation and Energy Production

The equine hindgut houses billions of microbes that break down fiber into usable energy sources through bacterial fermentation. The hindgut consists of the:

• Cecum: A fermentation chamber where microbes digest fiber.
• Large Colon: Continues fiber fermentation and absorbs water.
• Small Colon: Further absorbs water and electrolytes.
• Rectum: Expels waste material.

Disruptions in any part of the digestive process—whether due to diet changes, stress, or illness—can impact nutrient absorption, immune function, and overall health. For an in-depth look at the roles each part of the GI tract plays, read this overview of the horse digestive system.

What is the Gut Microbiome?

The gut microbiome is the community of microorganisms living within a horse’s GI tract. This population is also referred to as the gastrointestinal microbiota. It is present throughout the horse’s entire digestive system, but elements of the microbiota change gradually from one section to the next.

Organisms in the Gut Microbiome

• Bacteria: Assist in fiber, protein, and starch digestion, producing essential B vitamins and vitamin K.
• Fungi: Aid in breaking down complex fibers.
• Protozoa: May help process soluble carbohydrates.
• Archaea: Play a role in methane production.
• Viruses and Parasites: May create gastrointestinal disease.

Each horse has a gut microbiome that’s as unique as a fingerprint. It is influenced by factors such as diet (most importantly), age, weather, stress, illness, and medications. The microbiome begins developing at birth and is shaped by colostrum intake, environmental exposure, and early dietary changes.

Another way to think of the microbiome is to consider it as its own organ system. This system works to maintain digestive and immune health, is critical for normal gut function, and likely influences other parts of the horse’s body, such as the nervous system.

The Microbiome’s Impact on Immunity

The equine immune system and microbiome are deeply interconnected. The lymphatic system, a complex network of lymph vessels and nodes, acts as the highway for immune cells, helping the body recognize and combat threats. The lymphatic system plays the same role in both horses and humans, however, it is actually far larger and more complex in horses than in the human body. The equine lymphatic system balances fluid volume, assists in the absorption of fats, filters waste products and abnormal cells, and produces and releases immune cells.

Anything that alters the GI tract can affect the immune system. Research suggests that the diversity of microbiota may influence diseases and disorders, such as Equine Metabolic Syndrome (EMS). Research on horses with EMS shows distinct microbial differences than those of healthy, non-metabolic horses. However, further research is needed to fully understand these connections.

Microbiome-Gut-Brain Axis

Beyond immunity, the microbiome may also influence equine behavior through the microbiome-gut-brain axis (MGBA). This complex communication network links the nervous, immune, and endocrine systems. Changes in gut bacteria have been associated with behavioral shifts in horses, including:

• Anxiety and nervousness
• Spookiness or unpredictable reactions
• Stereotypic behaviors like cribbing, weaving, wood chewing, pawing, etc.

Factors like high-starch diets, chronic stress (including mental/emotional stress), and inconsistent routines can disrupt the microbial balance, potentially affecting a horse’s behavior and digestive processes. This can become a vicious cycle as disruptions to the microbiota may lead to behavioral issues, in turn further impacting the microbiota. These consequences could continue in this pattern. Understanding this connection may help horse owners manage both their horse’s gut health and temperament more effectively.

The Future of Microbiome Research

There are large gaps in our current understanding of the equine gut microbiome. However, there is research on humans that supports changes in the microbiome being associated with many diseases.

Nevertheless, advancements in technology are rapidly expanding our understanding. While early research on horses was limited to bacteria that could be cultured in a lab, new techniques for identifying types of organisms and sampling methods are emerging. Hopefully, future research and testing will allow scientists to analyze the full microbial community, as well as aim to:

• Identify how specific dietary changes influence microbial populations.
• Explore the microbiome’s role in disease resistance and immune function.
• Investigate potential treatments that support microbial health for various conditions.
• Develop strategies to combat drug-resistant infections and map the transmission of disease.

How Horse Owners Can Support Gut Health

Maintaining a well-balanced gut microbiome is key to strong immunity and overall well-being. So, how can we help our horses stay healthy? There are several strategies you can use to promote a healthy microbial balance in your horse’s gut, including:

• Provide High-Quality Forage: Ensuring your horse has consistent access to good sources of forage throughout the day that form the foundation of their diet.
• Consider Prebiotics and Probiotics: Prebiotics may help keep the microbiota in balance. Prebiotics are sources of non-digestive, soluble fiber that feed and nourish the live, beneficial microorganisms of the gut (probiotics). Combining pre- and probiotics may also be helpful, however, more supplement research is needed.
• Minimize Stress: Transport, competition, and changes in the herd can cause stress. Try to maintain as consistent a routine as possible to manage this. Maximizing the amount of time your horse spends in pasture turnout is also beneficial for gut motility, improving circulation, and mental well-being.
• Ensure Proper Hydration: Always provide access to clean, fresh water to support healthy digestion.
• Avoid Sudden Diet Shifts: Gradual feed transitions (over 7-10 days) may help the microbiome adapt without serious digestive upset.
• Monitor Health Changes: Pay attention to any changes in your horse’s appetite, manure consistency, or behavior which may signal microbial imbalances.
• Work Closely with a Veterinarian: Staying on top of regular wellness visits, parasite control, and vaccinations is key. When it comes to health issues, early intervention is always the best route.

Conclusion

The equine gut microbiome plays a crucial role in a horse’s overall health, influencing digestion, immunity, and temperament. By feeding a high-quality diet, reducing stress, and working closely with a veterinarian, owners can help keep their horse’s gut microbiome functioning as best it can. As scientists learn more about how gut microbes influence health, there may be new ways we can support digestion and immunity, helping horses live healthier, happier lives.

Evidence-Based Research

1. Elzinga, Sarah E., et al. “Comparison of the fecal microbiota in horses with equine metabolic syndrome and metabolically normal controls fed a similar all-forage diet.” Journal of Equine Veterinary Science, vol. 44, Sept. 2016, pp. 9–16, https://doi.org/10.1016/j.jevs.2016.05.010.
2. Chaucheyras-Durand, Frédérique, et al. “Gastro-intestinal microbiota in equines and its role in health and disease: The black box opens.” Microorganisms, vol. 10, no. 12, 19 Dec. 2022, p. 2517, https://doi.org/10.3390/microorganisms10122517.
3. Ang, Li, et al. “Gut microbiome characteristics in feral and domesticated horses from different geographic locations.” Communications Biology, vol. 5, no. 1, 25 Feb. 2022, https://doi.org/10.1038/s42003-022-03116-2.
4. Kauter, Anne et al. “The gut microbiome of horses: current research on equine enteral microbiota and future perspectives.” Animal microbiome vol. 1,1 14. 13 Nov. 2019, doi:10.1186/s42523-019-0013-3