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Equine Microbiome: Why Gut Microbiome is So Important and How Equine Nutrition Can Support the Intestinal Biome

Equine Microbiome: Why Gut Microbiome is So Important and How Equine Nutrition Can Support the Intestinal Biome

Equine Microbiome: Why Gut Microbiome is So Important and How Equine Nutrition Can Support the Intestinal Biome

What is a Microbiome?

The Biome is the name for the population of bacteria and other microbes which live in the GI tract of all animals.  These microbes can aid with digestion of food and have a great effect not only on digestion but also on many other aspects of health. We are only slowly coming to realize how many systems these bacteria have influence over, the immune system, metabolism, nerve function, and behavior are just a few of them.

There are a lot of different microbes in the biome, many thousands of different species, they live in different parts of the GI tract, and have influence not only on the part where they live but on other populations further down the tract.Some bacteria and fungi digest the incoming food and release metabolites from that digestion, these metabolites can be absorbed by the GI tract walls or by other bacteria.  They in turn digest and utilize the metabolites, and then release other metabolites, which can also be absorbed by both the GI tract and yet other bacteria.

Think of the biome as a web or network of bacteria and fungi, all busy absorbing and releasing metabolites.  We still don’t that much about the species that make up the biome, however increasingly we are discovering how much influence they have.  The microorganisms that make up the biome are referred to as the microbiota.

Human and Equine Microbiomes

So far we have learned that each animal (and human) have a unique set of diverse micro-organisms, an individual fingerprint. This means that not every animal or person reacts the same to a given diet or intake of food.  The interactions between the microorganisms are complex and multi-levelled, especially with respect to disease risks, health preservation, immune response, and therapeutic response.  Which in a nut-shell means that not all individuals will respond the same. This is an area of rapidly expanding research.

It should be realized that not all the organisms present in the biome are beneficial, some are capable of causing disease and can be harmful.  

All horses belong to a family of herbivorous mammals that posses a certain hindgut microbiota enabling forage utilization for optimal nutrition.  These microbes provide a substantial proportion of the horse’s daily energy needs through the fermentation of plant material to produce short chain fatty acids (acetate, butyrate and propionic). Consequently, disturbance of the in the equine microbiota can result in alteration of fermentation patterns and ultimately in metabolic disorders.  Horses host a huge number of bacteria within their GIT most of which reside in the caecum and colons. This fermentation of plant material by these microorganisms is crucial for the bioavailability of energy and other essential nutritional needs in horses.

In humans, the microbiota has been shown to have effects on cardiovascular disorders, inflammatory bowel disease, diabetes, rheumatoid arthritis, depression, and progression of cancer.  Much less is known in horses however there has been investigations in their impact on certain diseases, such as equine grass sickness, colitis and laminitis.

How to Support the Microbiome of the Horse

The effects of the equine microbiota has been much less studied, however we do know that they are essential for equine health and efficient digestion.  This is one reason it is important to change feedstuffs slowly over time, and not to feed too much sugar and simple starches.  The bacteria need time to adjust to the incoming feed, sudden changes lead to upsets in their relative populations and disturbances in the network.  This can result in an imbalance of the intermediary metabolites and subsequent negative consequences.

The microbiome of a horse, particularly in the intestine, plays a critical role in overall health, affecting everything from nutrient absorption to immune response. Supporting this microbial community is paramount for maintaining a healthy horse. The horse's gut microbiota is a diverse ecosystem composed of bacteria, archaea, and protozoa. These microbial inhabitants aid in breaking down food components that the horse cannot digest on its own, like certain fibrous plant materials. An imbalance, or dysbiosis, of these microbes can lead to a variety of health problems, including colic, a common and potentially life-threatening condition in horses.

The large intestine, also known as the hindgut, is a major hub of microbial activity. Here, gut bacteria ferment fibrous material into usable energy for the horse. The feces of the horse provide a snapshot of this microbial activity, making fecal microbiome analysis a valuable tool for assessing gut health in horses.

A healthy gut microbiota is balanced in diversity and abundance. For example, the bacterial species present in the intestine of a horse should not be overly dominated by any single type. One of the keys to microbiome support in horses is promoting this balance through diet and management practices.

Horses are designed to eat a fiber-rich diet, and their unique digestive system reflects this. The horse's gut, specifically the large intestine or hindgut, is a fermentation vat teeming with intestinal bacteria that break down fibrous plant materials like cellulose. As such, the best way to ensure the health of the biome is to make sure that the horse gets enough fiber in the diet, so that there is plenty of fiber for the microbiota to ferment and metabolize.   This also applies to humans BTW!

Feeding sufficient fiber is crucial to maintaining a healthy gut microbiota. The right kind of fiber, found in high-quality forage, feeds the beneficial bacteria in the horse's gut. These bacteria, in turn, produce volatile fatty acids like propionate, which serves as a significant energy source for adult horses. Conversely, a diet low in fiber can lead to intestinal dysbiosis - an imbalance in the gut bacteria. This imbalance can pave the way for pathogenic bacteria to proliferate, leading to a variety of health issues, including colic and laminitis.

The small intestine, though it plays a less significant role in fiber fermentation compared to the hindgut, is also impacted by the horse's diet. Adequate fiber intake helps prevent the overloading of the small intestine with undigested starch, a situation that can also favor the growth of pathogenic bacteria.

Horse feed rich in fiber, such as hay, grass, and beet pulp, encourages slow feeding and promotes better gut health by providing the necessary nutrients for beneficial bacterial growth. As equine research advances, horse owners are becoming increasingly aware of the importance of feeding sufficient fiber to ensure a healthy biome and optimal horse health.

The Role of Prebiotics and Probiotics

Prebiotics and probiotics are integral for supporting the gut microbiota and, by extension, the overall health of horses. Prebiotics are typically fibrous foods that serve as fuel for the beneficial bacteria in the horse's digestive tract. They stimulate the growth and activity of these bacteria, which in turn aids in the horse's digestion and nutrient absorption. Probiotics, on the other hand, are live beneficial bacteria or yeasts that are added to the horse's diet. These live microorganisms can help to restore balance in the gut microbiota, particularly after a period of stress or illness which may have caused dysbiosis.

In the case of horses, a carefully selected combination of prebiotics and probiotics can provide significant benefits. For instance, they can help maintain a stable population of beneficial bacteria in the large intestine, preventing the overgrowth of harmful microorganisms. The regular use of prebiotics and probiotics may also decrease the occurrence of colic, one of the most common disorders related to the digestive tract in horses.

By monitoring the gut microbiota, via feces analysis in horses, and supporting it with appropriate prebiotics and probiotics, we can optimize the health and well-being of our horses. In conclusion, understanding and managing the microbiome in horses is a crucial part of equine health and management.


The Equine biome consists of thousands of different bacteria, fungi, viruses and archaea. The health and well-being of horses are inextricably linked to their gut microbiota. The equine gut, particularly the large intestine, hosts a diverse community of microbes, including bacteria, archaea, and protozoa. These microbes play a critical role in nutrient extraction and health maintenance.

Disruption to this microbial balance, or dysbiosis, can cause health problems such as colic. Therefore, supporting the microbiome through practices like routine microbiome analysis in horses and administration of prebiotics and probiotics is crucial. The microbiota exist in most of the equine GI tract, but most importantly in the caecum and colons. The biome is essential for the health and well being of the horse. They contribute a significant amount of energy and other nutrients.

Further, horses are designed to consume a fiber-rich diet, and feeding sufficient fiber is key to maintaining gut health. Adequate fiber intake supports beneficial intestinal bacteria, prevents the proliferation of pathogenic bacteria, and contributes to overall horse health. The main way to ensure the health of the biome is to feed sufficient fiber. Changes to feed such as feeding grains should be done slowly and allow time for the biome to adjust.

Equine research continues to provide invaluable insights into the complexities of the equine intestinal tract, informing best practices for equine care. As horse owners, understanding and managing the microbiome of our horses is essential for their overall health and well-being. By paying careful attention to what we feed our horses and how we care for their digestive health, we can help ensure they lead healthy, happy lives.

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