In an influential study published in the Journal of Psychiatric Research, Kelly et al. (2016)3 transferred gut bacteria from patients with major depressive disorder into microbiota-depleted rats. The rats’ genetics, housing and diet remained unchanged. Yet after receiving the altered microbiota, they began to display behavioural and physiological features consistent with depression. The only difference was the microbial ecosystem in their gut.
This finding is not isolated. Across species, a consistent pattern keeps emerging: animals with behavioural disorders often show characteristic changes in their gut microbial populations. A recent systematic review by Homer et al. (2023)2, published in Animals, summarised evidence from production, performance and companion animals and reported recurring microbial alterations associated with behavioural abnormalities.
This has been reported in:
• Dogs with anxiety-related disorders
• Pigs exhibiting tail-biting behaviour
• Horses displaying stereotypies and hyperreactivity
Even more striking, horses with hyperresponsive and stereotypical behaviours have been reported to show microbiota changes resembling those described in patients with schizophrenia.
That does not mean horses have schizophrenia. It means overlapping biological signatures are being observed.
So what are these common microbial changes?
The Microbial Pattern Seen in Behavioural Disorders
Across species, animals with behavioural abnormalities tend to show:
• Reduced populations of fibre-digesting, butyrate-producing bacteria
• Increased lactic acid–producing bacteria
• Increased abundance of pro-inflammatory microbial groups
• Signs of reduced microbial diversity
Butyrate-producing bacteria are particularly important. Butyrate is a short-chain fatty acid that:
• Supports intestinal barrier integrity
• Reduces inflammatory signalling
• Influences gene expression
• Modulates neural immune cells (microglia)
When butyrate producers decline and lactic acid producers expand — a pattern often seen with high-starch feeding or stress — gut stability decreases and inflammatory tone increases.
Chronic low-grade inflammation is strongly associated with altered stress physiology and behavioural dysregulation in multiple species.
This microbial signature appears repeatedly in animals with stereotypies, hypervigilance, aggression and chronic stress behaviours2.
But why would bacteria in the hindgut influence behaviour at all?
For decades, that question would have sounded absurd.
The Gut Is Not Just a Digestive Organ
Traditionally, the equine hindgut was viewed purely as a fermentation chamber. Microbes break down fibre and produce volatile fatty acids that fuel the horse. End of story.
That view is now outdated.
The gut is part of an integrated communication network linking:
• The enteric nervous system
• The central nervous system
• The immune system
• The endocrine system
This bidirectional system is known as the gut–brain–immune axis.
And the key players in this communication are the microbes themselves.
How Can Gut Bacteria Influence the Brain?
The link between gut microbiota and behaviour is not mystical. It is biochemical.
The microbes living in the hindgut actively produce chemicals — including neurotransmitters and their precursors — that influence brain function. Some gut bacteria can manufacture neurotransmitters themselves, including GABA, dopamine and norepinephrine, while others stimulate intestinal cells to produce serotonin. These molecules are central regulators of behaviour.
GABA is the brain’s primary calming signal. It dampens excessive neural activity and supports relaxation and behavioural stability.
Dopamine is involved in motivation, reward and goal-directed behaviour; it influences curiosity, drive and responsiveness to training.
Norepinephrine plays a key role in alertness and vigilance. It is closely tied to the stress response and helps determine how strongly an animal reacts to novelty or perceived threat.
Most of these molecules do not simply travel directly from the gut to the brain in large amounts. Instead, they influence the nervous system indirectly. They interact with the extensive nerve network embedded in the gut wall, communicate through the vagus nerve, and modify immune and hormonal signalling. All of these pathways feed into the central nervous system and help regulate how the horse responds to its environment.
Gut microbes also influence the availability of the building blocks required to make these neurotransmitters. Amino acids such as tryptophan, tyrosine and glutamate serve as precursors for serotonin, dopamine and GABA. Changes in microbial populations alter how much of these precursors remain available for absorption and use. When the microbial balance shifts, the availability of these key compounds can shift as well.
Finally, microbes produce short-chain fatty acids such as butyrate, which help maintain intestinal barrier integrity and regulate inflammation. When microbial balance is disrupted, inflammatory signalling can increase. Chronic low-grade inflammation is closely linked to altered stress physiology and heightened behavioural reactivity across species.
Put simply: change the microbial community, and you change the chemical environment that helps regulate stress, alertness and behavioural stability. This biological framework helps explain why similar microbial shifts are observed in animals with behavioural disorders.
Diet: A Way to Shift the Microbiome
If the microbiota influences behaviour, then diet becomes highly relevant — because diet is one of the most powerful modulators of the gut ecosystem.
In a controlled crossover study published in Scientific Reports, Bulmer and colleagues (2019)1 fed ponies either a high-starch or a high-fibre diet, with management otherwise unchanged.
When fed the higher-starch ration, ponies:
• Changed pace more frequently
• Appeared more vigilant
• Spent less time calmly investigating
• Were assessed as more nervous and tense
When fed the high-fibre ration, the same ponies were more settled and exploratory.
At the same time, their gut microbiota shifted significantly. The high-starch diet reduced fibrolytic butyrate-producing bacteria and increased lactic acid–producing bacteria.
Behavioural reactivity and microbial composition moved together.
Importantly, the starch levels were within commonly recommended limits. This was not extreme grain overload.
The study does not prove that microbial changes caused the behavioural changes.
It does show that realistic dietary shifts alter both microbial composition and behavioural reactivity in parallel.
What This Means for Horse Owners and Trainers
For decades, behavioural issues were explained almost exclusively through training, temperament or past experience. Those factors unquestionably matter. But they are not the whole story.
In clinical practice, I frequently see behavioural concerns that cannot be fully explained by training or management alone.
Growing scientific evidence indicates that the gut microbiota plays an important role in regulating stress physiology, behaviour and neurochemical balance. This means that behavioural changes may sometimes have a physiological component rooted in the hindgut.
These insights carry practical implications:
- Prioritise forage as the foundation of the diet.
Fibre supports microbial diversity and butyrate-producing bacteria associated with gut stability. - Avoid unnecessary high-starch feeding patterns.
Even commonly recommended starch levels can increase behavioural reactivity in some horses.
- Introduce dietary changes gradually.
Abrupt feed transitions disrupt microbial balance and may alter stress responsiveness.
- Consider hindgut health when managing behavioural issues.
In cases of stereotypies, hyperreactivity or unexplained tension, evaluate forage quality, meal size, feeding frequency and overall gastrointestinal stability alongside training and environmental factors.
- Rule out physiological drivers before labelling a horse as “difficult.”
Pain, inflammation and altered gut microbiota can all influence behaviour.
None of this replaces correct training, adequate turnout, social interaction or environmental enrichment. Behaviour is multifactorial, and management must always be holistic.
Gut health, however, is an important part of that larger picture and deserves thoughtful consideration.
What We Know — and What We Are Still Learning
Research into the gut–brain–immune axis is advancing rapidly in human medicine and is increasingly expanding into veterinary science. In horses, however, the field is still developing. Large-scale mechanistic trials remain limited, and the biological complexity of the gut–brain–immune network makes research technically demanding. The unique nature of the equine hindgut — supporting an extensive and highly active microbial population — adds further layers of complexity.
Many mechanistic details therefore remain unresolved. Causality has not been definitively established. We still cannot say with certainty whether microbial changes drive behavioural alterations, or whether shifts in stress physiology and behaviour reshape the microbiota. The classic question remains: which comes first?
Yet despite these uncertainties, several conclusions are consistently supported by current evidence.
Animals with behavioural anomalies repeatedly show altered gut microbiota with specific and recurring patterns. Stress itself modifies microbial composition. Diet directly and reliably reshapes the microbiome. And when diet changes the microbial ecosystem, behavioural expression can change alongside it. In controlled feeding studies comparing high-starch and high-fibre diets, measurable behavioural differences were observed within just 14 days.
The direction of causality may not be fully resolved, but the association between behaviour and gut microbial composition is clear and reproducible.
For horse owners and trainers — and ultimately for the horses themselves — this is not a minor detail.
Mental welfare, behaviour and gut health are biologically intertwined. Maintaining a healthy gut microbiome is therefore not only essential for sound digestive function, but may also play an important role in supporting emotional and behavioural stability.
References
- Bulmer, L.S., Murray, J.A., Burns, N.M., et al. (2019). High-starch diets alter equine faecal microbiota and increase behavioural reactivity. Scientific Reports, 9, 18621. https://doi.org/10.1038/s41598-019-54039-8
- Homer, B., Judd, J., Mohammadi Dehcheshmeh, M., Ebrahimie, E., & Trott, D.J. (2023). Gut microbiota and behavioural issues in production, performance, and companion animals: A systematic review. Animals, 13(9), 1458. https://doi.org/10.3390/ani13091458
- Kelly, J.R., Borre, Y., O’Brien, C., et al. (2016). Transferring the blues: Depression-associated gut microbiota induces neurobehavioural changes in the rat. Journal of Psychiatric Research, 82, 109–118. https://doi.org/10.1016/j.jpsychires.2016.07.019