More microbes than genes?

The influence of the microbiome on genetic potential and athletic performance

“Most large animals in fact are not the single individuals they seem to be. They are walking menageries, whole communities of different species which, in their various ways are committed by evolution, for better or for worse, in sickness and in health, to live together.” – Sir David Attenborough

The presence of a diverse and highly individualised community of microorganisms within the gut and the environment they inhabit – collectively known as the microbiome – is now widely recognised in both humans and animals. Much like a fingerprint, each individual’s microbiome is unique. This microbial ecosystem plays a critical role in regulating host physiology. Moreover, it influences health, disease susceptibility and athletic performance.

The relationship between the gut microbiome and gene expression is complex and dynamic. In equine science, there is growing interest in how the hindgut microbiome might play a role in modulating genes associated with athletic performance.

Microbial metabolites: small molecules, big impact

Microbes in the gut produce a wide range of compounds called metabolites that act like messengers in the body, interacting with the horse to influence gene expression.  Some of the most influential of these metabolites are short-chain fatty acids (SCFAs), certain vitamins and some of the building blocks for neurotransmitters like GABA and dopamine.

Butyrate and propionate are two key SCFAs produced when fibre is broken down in the hindgut. These metabolites are increasingly linked to improved muscle function, more efficient energy use, immune regulation, faster recovery in athletic horses and improved markers of gut health.

The gut microbiome also communicates with the nervous system through the gut-brain axis. This two-way link can influence gene expression in the brain, affecting behaviour, stress responses and cognitive function – all of which play a role in training and performance.

Influencing epigenetics

Factors like diet, exercise, stress, stable management, developmental conditions and disease can all shape how genes are expressed because of their direct influence on the microbiome and the metabolites that it produces. This may help explain why two horses with similar genetics can perform very differently.  

In early life, the state of the microbiome has a particular effect on epigenetics and what genes are switched on or off, in addition to having a significant influence throughout the rest of their lives.  

As such, supporting an optimal microbiome environment is critical to ensure more favourable metabolites are produced to support optimal gene expression. 

For example, butyrate (produced by fibre-digesting microbes) is known to support normal cell function and energy use by influencing how genes are expressed.

Microbiome profiles in high-performing horses

Research shows that the composition of the equine hindgut microbiome differs between higher and lower performing horses. Fibre digesting microbes such as Firmicutes and Bacteriodetes (which produce more favourable metabolites) have been associated with improved performance outcomes. 

Alongside this, distinct patterns of gene activity have also been identified in high-performing horses, particularly those linked to energy metabolism, muscle development and response to physical stress. 

Epigenetic regulation plays a role in muscle development, metabolic efficiency, injury response and adaptation to training. For example, epigenetic modifications can influence muscle fibre composition and mitochondrial function, directly affecting strength, endurance and energy utilisation. Similarly, the regulation of genes involved in inflammation and tissue repair can impact recovery and long-term soundness.

Epigenetic variation (the difference in gene expression due to epigenetic influence) may help to explain why some horses fail to reach their apparent genetic potential. Differences in developmental programming – shaped by factors such as maternal nutrition and early-life environment – can have lasting effects on gene expression. Likewise, individual variability in epigenetic responses to training, injury, and metabolic demands can result in significant differences in performance, even among genetically similar horses.

Supporting performance potential

Its role in epigenetics and gene expression only further emphasises the importance of supporting the hindgut microbiome. 

Equine performance is shaped by complex interactions between genetics, epigenetics and the hindgut microbiome. The microbiome acts as a link between what a horse experiences (like diet, training, environment and stress), their genome (genetic material) and how genes are expressed. 

No two horses are the same, so strategic nutritional management based on individual microbiome variability could offer a practical and accessible means of influencing these pathways. A deeper understanding in this area of study offers promising opportunities to develop practical, more personalised approaches to training and management.