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Anxiety and Pain In Horses, the Microbe-Gut-Brain Axis

Updated: Feb 2

Pain and anxiety in horses is sadly quite common, and the underlying cause can be very difficult to detect. They can be triggered by illness or injury, bad experiences (or memories of a bad / frightening experience), poorly fitting tack, diet or management. Not only is this bad for the horse; pain and anxiety can lead to difficult or dangerous behaviour when ridden or on the ground.

If your horse has a sudden temperament change and becomes anxious and difficult to manage and ride, a health problem is the immediate suspect. Gastric ulcers and teeth are the two most common ailments, but the checklist also includes sub-clinical lameness, arthritis, injuries, and food sensitivities. The saying “teeth, back and tack” is commonly used as a starting point for owners whose horses are exhibiting the signs of pain or anxiety.


Strangely, the part of the anatomy often left off the health checklist is the hindgut. However, this part of the horse is thought to be the biggest contributor to the onset of anxiety and pain.

This article explores the relationship between the microbiome, the gut and the brain in relation to anxiety and pain in horses.

What is the Equine Hindgut?

The horse’s digestive system is made up of two main sections: the foregut and the hindgut. But what exactly is the equine hindgut, and how does it differ from the foregut?

The foregut consists of the oesophagus, stomach and small intestines. Meanwhile, the hindgut is made up of the caecum, large colon, small colon and the rectum. 

The foregut is relatively small when compared with the hindgut. Digestion in the foregut is rapid and minimal, and most of the important, slow fermenting digestion happens in the hindgut. The stomach holds 3-5 gallons or 18 L and is 9% of the total gastrointestinal tract, whilst the hindgut is eight metres long, holds 269.4 gallons (1,225 litres) of digesta, and makes up 61% of the total gastrointestinal tract.

The equine hindgut houses a microbial population that is able to break down indigestible fibre, which may be as much as 60% of the horse's diet. Therefore, the horse’s hindgut is a crucial part of the digestive system.

What is the gut-brain axis?

The gut-brain axis is a signalling or communication system that allows the gut to talk to the brain and vice versa. The two organs talk to each other by way of the immune system, the hormonal and the nervous system.

What is the microbe-gut-brain axis?

More recently, the gut bacteria that reside in the gastrointestinal tract of all mammals has been identified as the major component in the gut-brain communication system.

The microbe-gut-brain axis is more extensive than the gut-brain axis and includes immune cells, glands, gut, the nervous system, hormones, intestinal bacteria, and the brain.

The main purpose of this axis is to maintain balance (homeostasis) - a steady state able to provide the best functioning conditions of the gastrointestinal tract.   

When an imbalance in the microbe-gut-brain axis occurs, an opportunity for disease or discomfort is created. This can be all gastric discomfort syndromes including colic and colitis, the onset of obesity, EMS and laminitis, and gastric pain. It can also include other parts of the body such as the musculoskeletal system.

Where Does It Wrong?

Muscular or joint pain, anxiety, and nervousness are common in horses. New research has indicated the onset may originate from an imbalanced microbial community in the hindgut causing changes through the microbe-gut-brain axis.

The microbe-gut-brain axis is crucial for creating and maintaining the health of the entire body. If the balance within the gut bacteria community is altered (through diet/medication/environmental stress) the result can be an increased production of chemicals that affect the nervous system, promoting pain and sensitivity (Malatji et al 2017).

The gut profile of horses with chronic pain.

Gut bacteria can produce secondary metabolites (chemicals) that support good health or that are detrimental to good health. Too many bacteria producing toxic/harmful chemicals will alter the homeostasis (health balance) of the whole animal and will cause symptoms to appear in other organs of the body away from the gut as they react to higher levels of chemicals that aren’t good for them.

Though all the bacteria listed below are part of the core family of microbes present in most animals, an increase of any within those listed causes an imbalance within the community that can have devastating effects on the homeostasis of the gut and the rest of the body.

Which Types of Gut Bacteria Can Cause Issues?

In high levels, these types of gut bacteria can cause issues in horses:

1. Eubacterium, Faecalibacterium prausnitzii, Ruminococcus, Clostridium, and Actinomycetaceae: These bacteria reside predominantly in the small intestine and whilst hippuric acid production is a normal and important part of metabolism, an excess (can be measured in urine) is an indication of an unnatural (detoxification) process by the gut.

2. Higher percentages of Fusobacteria nucleatum and faecalbacterium causing an increase in 2-hydroxyisobutyric. This is the most damaging of the three chemicals to be produced. Higher levels of fusobacteria only occur in horses under stress. A higher percentage of fusobacteria are also linked to Inflammation of the hindgut. 2-Hydroxyisobutyric acid is chemically similar to lactic acid.

3. Higher levels of lactic acid-producing bacteria such as lactobacillus. Lactic acid production is part of many metabolic and biochemical processes in all mammals, but increases in lactic acid production are linked to illness, trauma, or poor diet. A rise in the last two chemicals sets up a process to restore a normal pH away from the acidic environment but in the process causes the release and increase of chemicals that irritate the nervous system triggering pain and fatigue.

What Long Term Changes Can Be Caused by Gut Imbalance?

If the gut imbalance isn’t rectified then the persistent, chronic noxious stimulant produced by the metabolites mentioned above can sensitise the nervous system and eventually make 3 long-term changes that cause chronic pain to perpetuate.

The changes to the nervous system include:

  1. The growth of extra nerves

  2. Nerves that increase their area of innervation (creating oversensitivity to touch)

  3. The nerves become more sensitive to the pain stimulus

Rebalancing the Microbial Population of the Gut

Whilst there is no single “ideal” or “perfect” balance of the hind gut microbiome, having a healthy, diverse balance in the microbial population of the gut can support the horse’s overall health and wellbeing.

Increasing the Diversity Score in the Horse's Hindgut

Biodiversity within the gut microbial community is measured using the Shannon Index. Having a good score is correlated to a healthy gut community and resilience against disease and allergies. Having a diverse and varied population will ensure healthy digestion, with enough beneficial microbes to help absorb essential nutrients and regulate the immune, metabolic, and nervous systems. A high (in the green) Shannon Index score means a healthier animal. 

The Shannon Index is a mathematical calculation of the number of different species in the sample, ranging from 800-1,500 for horses.

This is combined with an equation to measure the proportion or richness of the species, i.e. how many of each different species there are and how many there are in comparison to other bacteria.

For example: If one species of bacteria is present in high numbers, perhaps accounting for 80% of the microbiome, and there are 800 species in total, the rest would be present at very low percentages eg. 0.001% of the biome. The result would be a lower biodiversity score. A higher Shannon Index score would indicate a greater number of individual species and a more even representation of them in the gut.

The EquiBiome Gut Analysis will give an accurate biodiversity score and the report will describe how to restore health through dietary changes. You can find out more about the importance of microbiome diversity in this article.

Help for Your Horse

It can be difficult to decide whether the hindgut might be involved in the symptoms of anxiety and pain, if you are unsure and would like some help and support, please contact us, we'd love to talk to you! or

or phone 01248872506

EquiBiome Equine Faecal Test Kits

Our equine faecal test kits come with instructions and are straightforward to use. Our customers include owners of horses with various conditions, including EMS, sarcoids, laminitis, obesity and more. Our database includes horses of various ages, breeds, types and disciplines, helping us to better understand equine hindgut health. 

If your horse is experiencing chronic pain or anxiety, taking the EquiBiome test may highlight an imbalance in the microbial community. The results of the test can help inform you of how and what to feed your horse to help support a healthy microbial gut community.

It can be difficult to decide whether the hindgut might be involved in the symptoms of anxiety and pain. If you are unsure and would like some help and support, please contact us. We'd love to talk to you!

Please note: EquiBiome is not intended to diagnose, treat or cure any condition. or phone 01248872506   

A.S. Santos, M.A.M. Rodrigues, R.J.B. Bessa, L.M. Ferreira, W. Martin-Rosset,

Understanding the equine cecum-colon ecosystem: current knowledge and future perspectives,

Animal, Volume 5, Issue 1, 2011, Pages 48-56, ISSN 1751-7311,

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