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The Microbiome, Hind Gut Ulcers and the Effects of Stress

Updated: Sep 15, 2023

About the hind gut

Gastrointestinal diseases and upsets are common in horses, causing discomfort, loss of performance, and even death. Every common gastrointestinal disease can be linked back to disturbances (dysbiosis) of the gut bacteria.

New gene technology is driving research at an intense rate, providing new insights into the equine microbial community, and providing both the horse owner and the vet with a powerful and accurate analytical tool to improve health and manage disease.

The gut bacteria community.

The gastrointestinal tract of the horse is colonized by trillions of microorganisms, which include 1,000-1,500 different species, making up around 95% of the biome; the other 5% are made up of archaea, protozoa, fungi, and viruses. The microbial community has co-evolved with the host, performing essential and vital activities such as the extraction of energy and nutrients from foodstuff, synthesis of vitamins, interaction with the immune system, and crosstalk with the brain, which is thought to affect temperament and behaviour.

Taxonomic and functional compositions of the gut microbiome are rapidly becoming viable indicators of horse health and disease. Each member of the microbial community has a different but synergistic role, being of benefit to the health of the horse, e.g., the fungi break down the indigestible parts of forage plants, such as the polysaccharides, while the ciliate protozoa contribute by producing a wide range of enzymes that the horse is unable to manufacture, and which benefit the immune system. Microbial fermentation of cellulose, hemicellulose, and lignin reduces the structural and non-structural plant wall material into carbohydrates, proteins (amino acids) and lipids, and produces volatile and short-chain fatty acids, which are the primary source of energy for the horse.

The bacteria community contributes the most to the degradation of ingested food, producing the final components of the fermentation process, which are acetic, propionic, butyric acid, methane, and carbon dioxide. The gastrointestinal tract of the horse is sensitive to change, stress, environment, and medication, which cause imbalances or dysbiosis.

Hind gut fact

The predominantly indigestible components of the equine diet are digested by the gut microbes that reside in the hind gut.

Cellulose, hemicelluloses, and pectins are resistant to the horse's hydrolytic enzymes and only enzymes produced by the bacteria can break them down.

The hindgut has a special holding area called the caecum to arrest the passage of digesta through the gut to allow time for the microbes to do their job.

The Fermenting Process

The fermenting process is a slower process compared to the rapid release of energy from easily degradable starch taking place in the foregut. Fermented energy takes time to produce, but this method allows him to survive the winters in the wild, when food (especially starch) may be hard to come by.

The horse is designed to consume large amounts of highly degradable starch in the spring and summer, which he needs for breeding, galloping, feeding young and storing up energy in fat deposits to use in the winter. Then when food is scarce he relies upon the fermentation process in the hind gut to produce energy much more slowly.

In other words, he has two survival systems in place, perfectly matched to provide rapid energy (for moving at speed and breeding) and to produce slower energy during times when food is scarce.

Getting the balance right for a modern stabled horse, can be challenging and metabolic imbalances such as laminitis, obesity, ems, ulcers, colic and acidosis of the hind gut are very common, the microbes of the gastro intestinal tract are very sensitive to changes in pH. If the degradable starch levels are higher than the slower release fibrous material, then the lactic acid loving bacteria can outnumber the acid eating members of the gut biota and the horse is then susceptible to low grade continuous acidosis, leading to the previously mentioned modern metabolic dysfunctions.

Good fermentation patterns contribute to good gut health, it depends on........


  • Higher numbers of lactic acid bacteria in the upper G.I. tract including Proteobacteria, and Bacteroidetes, able to rapidly degrade carbohydrates, amino acids, and proteins.

  • Only complex carbohydrates reaching the hindgut.

  • In the hindgut or lower G.I. tract, Firmicutes, Bacteroidetes, Fibrobacteres to ferment the complex carbohydrates to make short-chain fatty acids.

Imbalances occur when the proportions of the core members either increase or decrease due to a number of stressors.

Stressors include dietary, early life management, transportation, long-term medication, anthelmintics, and training/competing in sports.

The microbiome profile of horses with gastrointestinal diseases is different from healthy horses. The three differences are.

  1. A reduction in diversity

  2. A change in the Firmicute/Bacteroides ratio

  3. An increase in inflammatory pathogenic bacteria.

The microbial community plays a critical role in maintaining the horse’s health. New microbiological technology has allowed us to identify the bacteria that alter fermentation patterns causing imbalances (dysbiosis). Park et al., (2021) examined the microbial populations of horses with gastric disease and those without, using the same technology as the EquiBiome analysis (16S rRNA sequencing from faecal samples). The horses with intestinal disease had lower diversity than horses that were healthy, lactic acid bacteria, Lachnospiraceae, and Lactobacillaceae were overgrown in horses with large intestinal colic. Stabling and diet also reduce diversity. The Equibiome Analysis gives a diversity score based on the Shannon Index and offers advice on how to increase the score.

Rebalancing the microbiome of horses with any of the above profiles has 3 targeted steps - 1. Feeding the good gut bacteria make the microbiome less favourable for the pathogenic bacteria together with feeding a natural antimicrobial (tannin, saponin, polyphenols). 2. Avoid the use of a lactobacillus/bifidobacteria probiotic as both increase in horses with the gastric disease profiles described above. 3. Reducing the bacteria that produce lactic acid.

A bit more on polyphenols

Polyphenols are a large family of natural compounds, they have a multitude of interactive biological activities and have great potential as therapies/food to improve the biome.

A polyphenol is a plant chemical found in the outer layers of the leaves and stems of most plants. They can also be aromatic, found in the flowers and the fruits/seeds of wild plants, the equine gut is specially designed to break down the hard- outer area of seeds and stems. There are over 8,000 different polyphenols, many but not all are easily absorbed through the equine G.I. tract, most are absorbed in the fermentation vat called the cecum.

In humans, the polyphenol contribution to health is noted and consumption of tea, wine, fruits, vegetables, and extra virgin olive oil are encouraged and promoted as an antidote to many diseases including diabetes type 2, I/R and obesity. Interest from equine nutritionists is low with more focus on the importance of a balanced vitamin and mineral content of the diet with little to no information on the links to health from the dietary addition of polyphenols.

Freely grazing, feral or wild horses have access to polyphenols from seeds, flowers and fruits of wild shrubs, grasses and herbs, the richest polyphenols are found in diverse meadows and pasturelands.

Take Home Tips

A triple SI field (Site of special scientific interest) will yield an estimated 500 different polyphenol compounds, whilst the average equine pasture provides only 30-40.

Polyphenols are best fed fresh from the field or from hay.

One of the old rules of feeding used to be to feed good quality hay with the seed head intact and the colour of the flowering head retained…. This will provide a range of polyphenols to the diet, simply put and easy to understand.

Milk Thistle is among one of the most well-known containing silymarin and quercetin. There is plenty of evidence to link high glucose levels with oxidative stress, inflammation, and poor insulin regulation. Polyphenols protect against the effects of hyperglycemia and improve glucose metabolism.

Some polyphenols (tannins and saponins) are not well digested and therefore remain at high levels in the gastrointestinal tract where they reduce the bacteria linked to inflammation and increase the bacteria linked to good metabolism.

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