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Good vs Bad Gut Bacteria in Horses

The equine microbiome is a fascinating subject, and horses can have a range of different good and bad bacteria present in the hind gut. This blog article explores the roles of good gut bacteria, why “bad” bacteria is bad, and whether it is possible for a horse to have too much “good” bacteria. 


This article covers:


What Makes “Good” Bacteria Good for Equine Digestive Health?

We often hear about “good” bacteria in human and equine health. But what does this actually mean? A healthy balance of good bacteria has a range of benefits for the horse’s overall health and wellbeing, and it starts in the digestive system.


Good bacteria play a crucial role in the horse’s digestive system. The equine digestive system can be split into two main sections: the foregut and the hindgut. The foregut, made up of the oesophagus, stomach and small intestine, is responsible for initial digestion. The hindgut, which includes the large intestines, is responsible for the slow digestion of fibres.


The good bacteria found in the equine hindgut contribute to the breakdown of complex carbohydrates, ensuring the efficient extraction of nutrients from the horse's diet. These good bacteria are essential for fermenting fibrous plant materials, a process that yields short-chain fatty acids (SCFAs). SCFAs are a crucial energy source for the horse and also play a role in maintaining the health of the gut lining. A well-nourished gut lining acts as a barrier, preventing harmful substances from entering the bloodstream and causing systemic issues.


Why Bad Bacteria Are Bad

While good bacteria are beneficial to the equine microbiome and the horse’s overall health, the presence of harmful bacteria can pose a threat. Disruptions in the balance between good and bad bacteria can lead to a range of digestive disorders and impact your horse's overall well-being.


Common culprits include pathogenic bacteria like Salmonella and Clostridium, which can cause gastrointestinal issues. 


Can a Horse Have Too Much Good Bacteria?

It is possible to have “too much of a good thing”. An excessive population of one type of beneficial bacteria can disrupt the delicate balance within the microbiome and lead to various health issues. This bacterial imbalance is known as gut dysbiosis, which has been associated with colic. Colic is a leading cause of mortality in horses.


Below are a number of other issues that may occur as a result of an overgrowth of good bacteria:


Fermentation overload can occur when an excessive fermentation process leads to an overproduction of short-chain fatty acids (SCFAs). Whilst this fermentation process is normal and essential to a horse’s digestion, too much can overwhelm the digestive system.


Overpopulation of one type of good bacteria could alter the pH balance in the horse’s hindgut. As a result, the environment becomes less favourable for other essential microbes. This can impact the efficiency of enzymatic processes and nutrient absorption.


An overabundance of one type of good bacteria may lead to a nutrient deficiency or excess. Different bacteria contribute to the synthesis of different nutrients, so it is important to have a balance of different types of good bacteria to ensure the horse receives all of the required nutrients in the right amounts.


An imbalance in the microbiome can trigger an inflammatory response, even if the bacteria involved are generally beneficial. Chronic inflammation may compromise the horse's immune system and contribute to a variety of health issues.


The gut lining plays a crucial role in maintaining a barrier between the digestive contents and the bloodstream. An overabundance of bacteria may stress the gut lining, compromising its integrity. This stress can lead to leaky gut syndrome, allowing harmful substances to enter the bloodstream and potentially causing systemic issues.


Preventing Gut Dysbiosis in Horses

To prevent the overgrowth of beneficial bacteria, it's essential for horse owners to focus on maintaining a balanced and varied diet, avoiding abrupt dietary changes, and monitoring the horse's health and behaviour. Regular faecal testing, as offered by services like EquiBiome, can provide valuable insights into the composition of the microbiome, helping horse owners make informed decisions about their horse's diet and overall care.


Factors That Affect the Microbiome

There is no single ideal or perfect microbiome. The microbiome will vary between individuals, with age, breed and discipline or work intensity all having a role. However, an imbalance of the microbiome is common in horses and it can affect the horse’s health, as we have discussed. 


There are a range of factors that may affect the balance of the microbiome, including sudden changes in diet, stress, the use of antibiotics, wormers or NSAIDs. Being aware of how you are feeding and managing your horse, and the medications they are on, can help you to monitor, understand and manage potential imbalances.


Monitoring your horse’s hind gut bacteria with the EquiBiome test can help you understand changes in your horse’s microbiome. This in turn can help you to make adjustments to your horse’s diet to help support a healthy, balanced microbiome.


Antibiotics & Antibiotic Resistance

The use - and misuse - of antibiotics and wormers is a growing concern with resistance on the rise. Ensuring that you only administer antibiotics exactly as prescribed by your vet and always completing the prescribed course of antibiotics is crucial in the fight against antibiotic resistance. Targeted worming based on regular faecal worm egg counts is also very important, as it ensures that your horse is wormed correctly and only when they require worming.


Of course, this is not to say that we should never use antibiotics or wormers. When prescribed and administered properly, they are an important - even lifesaving - part of equine medicine.


How to Support a Healthy Microbiome

We have explored the dynamics between good and bad bacteria in the equine microbiome, so now we will turn our attention to actionable strategies for promoting good equine gut health.


A balanced diet that meets your horse’s nutritional needs is key to equine gut health. Hay / haylage, grass and a low-sugar, high-fibre feed will form the mainstay of most horses’ diets (depending on their specific requirements). However, herbs, other plants and supplements may also help to support a healthy, balanced, microbiome. If you need to make any changes to your horse’s diet, it is important to do this gradually to minimise stress on the digestive system.


Adding prebiotics and probiotics to your horse’s diet can also help to support a healthy digestive system and microbiome. Prebiotics help to support beneficial bacteria, whilst probiotics introduce live cultures.


Regularly monitoring your horse’s gut bacteria with the EquiBiome test can help you to understand your horse’s hind gut health and how your horse’s diet or management may be impacting their health.


EquiBiome: Empowering Horse Owners

By taking a proactive approach to your horse's gut health, you empower yourself to make informed decisions that support wellbeing. EquiBiome's faecal tests offer a window into your horse's microbiome, taking the guesswork out of what and how to feed your horse.


The equine microbiome significantly influences your horse’s health and wellbeing. By understanding the delicate balance between good and bad bacteria, horse owners can be better informed of how diet, management and medication affects their horse’s health. Through a holistic approach that encompasses nutrition, management, and regular monitoring, you can take steps to support a balanced microbiome.


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