Unlocking the Secrets of Equine Gut Health: Evolutionary Microbiome Dynamics and Modern Challenges

March 20, 2024

By Sarah Griffiths, DCH

In the vast expanse of equine evolution, one of the most fascinating tales lies within the hind gut – a vital aspect of the horse’s digestive system. From the expansive cecum to the intricate microbiome within, the evolutionary journey of the equine hind gut unveils secrets crucial for understanding the dietary needs of our modern-day companions.

Evolutionary Roots: The Equine Hind Gut and Cecum

Millions of years of evolution have sculpted the equine hind gut into a marvel of efficiency. At the heart of this system lies the cecum – a large, pouch-like structure where fermentation of fibrous plant material occurs (Dougal et al., 2013). This fermentation process is facilitated by a diverse array of microorganisms, including bacteria, protozoa, and fungi, which break down cellulose and other complex carbohydrates into digestible nutrients (Daly et al., 2001).

Feral horses, roaming vast grasslands and plains, evolved alongside this digestive system, consuming fibrous plant material as their primary diet. The hind gut, finely tuned over millennia, efficiently extracted nutrients from these tough plant fibers, sustaining these majestic creatures in the wild.

Feral vs. Modern Equine Diets: A Disruptive Shift

The advent of domestication has ushered in significant changes to the equine diet. Modern equines are often fed diets high in processed grains and low in fibrous forage, a far cry from the natural grazing habits of their ancestors. This shift in dietary composition has profound implications for the hind gut microbiome.

Research utilizing DNA sequencing techniques has shed light on the plant diversity present in feral horse diets. Studies analyzing plant fragments in feral horse manure have revealed a diverse array of grasses, herbs, and shrubs, emphasizing the importance of a varied forage diet for maintaining gut health (Costa et al., 2012).

Microbial Communities in Domesticated vs. Feral Horses

Comparative studies between domesticated and feral horse populations have illuminated stark differences in hind gut microbiome composition. Feral horses exhibit greater microbial richness and diversity compared to their domestic counterparts (Costa et al., 2015). The shift from a natural forage-based diet to processed feeds and limited access to diverse grazing environments in domesticated settings contributes to this loss of microbial diversity.

Consequences of Dietary Shifts: Hind Gut Microbiome Impacts

The repercussions of these dietary shifts are starkly evident in the hind gut microbiome of domestic horses. Compared to their feral counterparts, domestic horses often exhibit reduced microbial diversity and richness in their hind guts (Dougal et al., 2013). This loss of diversity can lead to imbalances in gut flora, predisposing horses to a myriad of health issues, including colic, laminitis, and gastrointestinal disorders (Mackenzie & Hallowell, 2021).

Restoring Equine Gut Health: Ancestral Solutions for Modern Challenges

To combat the decline in hind gut microbiome diversity and richness, it is crucial to revisit the ancestral dietary requirements of horses. Emphasizing a diet rich in high-quality forage – mimicking the fibrous plant material consumed by feral horses – is paramount for maintaining gut health.

Practical Solutions for Equine Diet Optimization

For horse owners and equine health professionals alike, implementing dietary changes is key to restoring and maintaining gut health. Consider the following practical solutions:

  1. Increase and Diversify Forage Intake: Prioritize access to a diverse range of high-quality forage, natural environments, nutritive herbs, and living soil to promote hind gut fermentation and microbial diversity.
  2. Eliminate Highly Processed Feed and Grain Feeding: Extruded grain and legume-based feeds can disrupt hind gut flora balance.
  3. Eliminate Timed Feedings: Implement 24-hour slow-feeding techniques to mimic natural grazing behavior and promote prolonged digestion.
  4. Supplement Strategically: Incorporate diverse access to prebiotic fibers and probiotics into the diet to support a healthy hind gut microbiome.

Conclusion: Nurturing Equine Gut Health for Optimal Well-being

In the intricate tapestry of equine health, the hind gut microbiome plays a pivotal role. Understanding the evolutionary roots of the equine digestive system and its adaptations to a fibrous plant-based diet provides invaluable insights into modern dietary practices. By prioritizing forage-based diets and implementing targeted dietary interventions, horse owners and equine health professionals can work together to restore and maintain the richness and diversity of the equine hind gut microbiome, ensuring the well-being of our cherished companions for generations to come.

Want to learn more about how to prevent common dietary diseases and improve your horses diet? Take my new mini course: Concepts in Holistic Equine Nutrition for 5 Modules to help you level up your horses health. You can even watch the first module for free here


Costa, M. C., Arroyo, L. G., Allen-Vercoe, E., Stampfli, H. R., Kim, P. T., Sturgeon, A., … & Weese, J. S. (2012). Comparison of the fecal microbiota of feral and domestic horses. PLoS ONE, 7(8), e40631.

Daly, K., Stewart, C. S., Flint, H. J., & Shirazi-Beechey, S. P. (2001). Bacterial diversity within the equine large intestine as revealed by molecular analysis of cloned 16S rRNA genes. FEMS Microbiology Ecology, 38(2-3), 141-151.

Dougal, K., de la Fuente, G., Harris, P. A., Girdwood, S. E., Pinloche, E., Geor, R. J., … & Newbold, C. J. (2013). Characterisation of the faecal bacterial community in adult and elderly horses fed a high fibre, high oil or high starch diet using 454 pyrosequencing. PLoS ONE, 8(10), e76573.

Mackenzie, J., & Hallowell, G. D. (2021). The horse’s microbiome and its potential role in equine gastrointestinal disease. Veterinary Clinics of North America: Equine Practice, 37(1), 1-13.