Lab To Stable Edition 6: Beyond the Gut: What Can Metabolomics Tell Us About the Effects of Prebiotics and Probiotics in Horses?

Prebiotics and probiotics have become increasingly popular in equine nutrition, often promoted for improving digestive health, supporting the gut microbiome, and enhancing overall wellbeing.

How do we know How if these supplements are actually working?

While improvements in consistency or digestibility provide some answers, they don’t reveal the complex biochemical changes taking place within the horse. This is wheremetabolomics is offering exciting new insights.

What Is Metabolomics?

Metabolomics is the comprehensive study of metabolites-the small molecules produced by both the horse and its gut microorganisms during metabolism.

Unlike microbiome studies, which identify which bacteria are present, metabolomics tells us ‘what those bacteria are doing’. By analysing metabolites in blood, faeces, urine, or saliva, researchers can gain a real-time understanding of how dietary interventions influence biological function.

In other words, metabolomics helps connect changes in the microbiome with measurable effects on the horse’s health.

How Do Prebiotics and Probiotics Influence the Metabolome?

Prebiotics provide substrates that stimulate the growth of beneficial microbes, while probiotics introduce live microorganisms that may help maintain a balanced gut ecosystem.

As these microbial populations change, so does the collection of metabolites they produce.

These include:

• Short-chain fatty acids (SCFAs) that support hindgut health and provide an important source of energy.
• Metabolites involved in amino acid metabolism, influencing protein utilisation and tissue repair.
• Compounds associated with lipid metabolism, which may affect energy balance and body condition.
• Metabolites linked to immune regulation and inflammatory responses.

Rather than simply observing changes in microbial composition, metabolomics enables researchers to measure these functional outcomes directly.

From Gut Health to Whole-Body Health

The effects of prebiotics and probiotics extend beyond digestion.

Microbial metabolites can influence communication between the gut and other organs through what is often referred to as the gut-organ axis. These biochemical signals may affect immune function, energy metabolism, exercise recovery, oxidative stress, and even metabolic health.

This means that nutritional interventions designed to support the gut may also have wider physiological benefits throughout the body.

Why Does This Matter for Equine Nutrition?

Traditional nutrition studies often evaluate supplements by measuring digestibility, growth, or performance.

Metabolomics adds another dimension by helping researchers understand how these supplements work.

For example, if a probiotic increases beneficial microbial metabolites associated with improved fibre fermentation or reduced inflammation, metabolomics can detect these changes long before clinical improvements become obvious.

Similarly, prebiotics may promote the production of metabolites that contribute to gut barrier function, nutrient utilisation, and metabolic stability.

This mechanistic understanding allows researchers to move beyond asking ‘whether’ a supplement works to exploring ‘why’ it works.

Towards Precision Nutrition

As metabolomics is increasingly combined with microbiome sequencing, researchers are gaining a more complete picture of how horses respond to dietary interventions.

Advanced analytical techniques such as LC-MS, GC-MS, and NMR spectroscopy allow hundreds of metabolites to be measured simultaneously, providing detailed insights into host-microbe interactions.

In the future, these technologies may support precision nutrition-where prebiotic and probiotic supplementation is tailored to an individual horse’s metabolic profile, health status, workload, and gut microbiome.

Future Direction

Prebiotics and probiotics are no longer viewed simply as digestive supplements. Their influence extends to the metabolic pathways that underpin health, performance, and disease resilience.

Metabolomics is helping us uncover these hidden biochemical responses, providing the evidence needed to better understand how nutritional interventions shape equine physiology.

As research continues to evolve, metabolomics has the potential to bridge the gap between the gut microbiome and practical feeding strategies, bringing us closer to personalised, evidence-based nutrition for every horse.