Increasing Microbial Diversity Wild Horses | BioStar US

Look to the Gut: Increasing Microbiome Diversity

The microbiome of the gut is a fascinating universe — one we are just beginning to understand. The complexities are vast, and we now know that imbalances within microbial communities have wide-reaching effects on our horses’ health. Research also tells us that greater microbiome diversity is essential to building and maintaining a healthy GI tract.

Did you know that…

  • specific probiotic strains can help regulate homeostasis of iron in the horse?
  • a microbial imbalance in the gut known as dysbiosis can affect inflammation, metabolism, concentration, focus, anxiety, and the formation of ulcers, particularly in the hindgut?
  • administering NSAIDs can directly impact the function and composition of the gut microbiota?

Iron metabolism and the gut

Iron Many horses are over-supplemented with iron. Over-supplementation usually occurs when a horse is diagnosed with anemia or lack of energy. However, iron supplementation does not increase energy. In fact, iron deficiency is the least common cause of anemia in horses.

Iron is one of the most abundant minerals in our soils and is readily available through grazing. When horses take in too much iron, either via supplementation or through feed, forage and hay, the iron overload can cause gut dysbiosis; having too much iron reduces the abundance of commensal bacteria and can stimulate the growth of pathogenic bacteria.

Iron availability is tightly regulated in the gut, where specific Lactobacillus probiotic strains such as L. reuteri are critical in modulating the secretion of mucin — a substance that binds to iron, helping to maintain iron homeostasis throughout the body.

Gut microbiota and metabolic syndrome

Microbiome Diversity Is Key to Horse Health | BioStar US New, compelling research shows that the balance and microbiome diversity among bacterial families in the large intestine can be disrupted or depleted in horses with Equine Metabolic Syndrome (EMS), as compared to horses that do not have EMS. 1, 2

Gut microbiota and inflammation

inflammation The gut microbiota and metabolites can regulate inflammatory conditions. Reports from researchers highlight the role of the gut microbiota in some inflammatory diseases such as asthma, diabetes, and obesity.

“Accumulating evidence indicates that alterations in the gut microbiota are responsible for the progression of obesity.” 3

Gut microbiota and the brain

brain illustrationThe gut and the brain communicate bi-directionally with each other. Dysbiosis of the gut microbiome affects not only the gastrointestinal system but also influences anxiety, lack of focus and concentration. Gut dysbiosis affects the hypothalamic-pituitary-adrenal (HPA) axis, which then stimulates the release of cortisol.

Chronic high levels of cortisol in horses can affect blood sugar levels, and the balance of neurotransmitters such as serotonin and dopamine.4

Gut microbiota and NSAIDs

NSAIDs bottleAccording to research at the Perelman School of Medicine at the University of Pennsylvania, gut bacterial composition shifted after clinically relevant doses of a non-steroidal anti-inflammatory drug (NSAID). That shift in bacterial composition favored the pro-inflammatory bacteria.5

Current research on microbial communities in horses

The main microbial communities in horses

One of the complexities of the gut microbiome is that every horse’s microbiome is unique to that horse. However, current research has shown that several main microbial communities exist in all domesticated equines.

Firmicutes is the largest phylum of the equine intestinal bacterial community. It includes Lactobacillus, Bacillus, Bifidus, and Clostridia.

The next largest group are the Bacteroidetes. This phylum of microbiota include both pathogens and beneficial species. They digest carbohydrates, producing short-chain acids: acetate and butyrate.

It’s interesting to note that a study comparing the fecal microbiomes of healthy horses and those with colitis showed that, in healthy horses, the microbiome ecosystem consisted primarily of Firmicutes, while the most abundant phylum for horses with colitis was Bacteroidetes.6

The next largest group are the Proteobacteria, including Enterobacteriales and Pseudomonadales. These bacteria are predominant in the small intestine, with the highest concentration found in the ileum. According to researchers, an overabundance of Proteobacteria is associated with inflammatory intestinal dysbiosis conditions such as colic.7

The fourth group consists of Verrucomicrobia. This phylum is found within the environment: soil, freshwater, and marine waters. It is particularly abundant in soil. These bacteria reside in the equine caecum, small colon, rectum, and feces. Verrucomicrobia help maintain the integrity of the mucin layer and decrease bowel inflammation.

Microbiome Diversity Is Key to Horse Health | BioStar US

Gut microbiota in feral versus domesticated horses

Two studies published in Nature evaluated the differences between the microbiota in feral horses versus domesticated horses.

The first study, published in 2017, focused on horses in Mongolia, where researchers sequenced the fecal microbiomes of both wild and domesticated horses. It was found that the microbiomes of the wild horses had more diversity of bacteria compared to domestic horses. Researchers also pointed out that the wild horses live in families, and that “social structure has a significant effect on the composition of horse fecal microbiomes.8

The second study, published in 2022, compared 57 domestic and feral horses from different locations on three continents.
The domestic/captive horse microbiomes were enriched with genes conferring resistance to tetracycline, likely reflecting the use of this antibiotic in the management of these animals.

Because of the common use of antibiotics in horses, the bacteria have responded by harboring resistance genes. The feral horses did not have bacteria with resistance to tetracycline.

Our data showed an impoverishment of the fecal microbiome in domestic horses with diet, antibiotic exposure and hygiene the likely drivers.

This study highlights that domestication and captivity reduce microbiome diversity. Another interesting observation is that carbohydrate metabolism enzymes were higher in feral horses than in domesticated horses.
Wild-living animals showed a potentially higher ability to catabolize complex carbohydrates, likely reflecting a more varied diet with a more complex and variable carbohydrate availability.

As these researchers re-emphasized in their conclusion: “[I]mpoverishment of the intestinal microbiota was observed in domestic horses compared to feral animals.9

Microbiome Diversity Is Key to Horse Health | BioStar US

Wild Mustangs

Increasing microbiome diversity in the gut

What the wild horses are teaching us is that their varied diet increases the microbiome diversity in the gut. How can we help the microbiome in our domesticated horses become more like that of their free-roaming relatives?

Adding forage

If you are feeding alfalfa pellets, add some Teff hay pellets (12% protein, 27% fiber, 8% NSC) to encourage more microbial diversity.

Probiotic supplementation

For many years I advocated using probiotics short-term to rebalance the gut microbial community, and then leaving it alone to self-perpetuate.

But now, I think daily probiotic support may be a necessity, particularly for horses in stalls, on limited turnout, limited fresh forage, in hard work, horses who compete and travel, and/or whose access to a variety of hays, fresh forages, and beneficial pasture herbs is limited.

1) Look for active probiotics that contain the Lactobacillus, Bifidum, and/or Bacillus strains.
Lactobacillus and Bifidum strains must be enteric coated or microencapsulated to ensure passage through the stomach. Otherwise, most of the bacteria will be destroyed by stomach acids.
Bacillus strains are spore-producing bacteria, and can survive the harsh environment of the stomach.

2) Saccharomyces yeasts are probiotics that work primarily in the hindgut by modulating the microflora, specifically cellulolytic bacteria, which digest fiber. Horses that struggle to maintain weight, older horses, and horses with fecal water syndrome, diarrhea, or leaky gut can benefit from yeast probiotics. Yeasts such as S. cerevisiae and S. boulardii are hardy and do not need microencapsulation.


There are still so many things we don’t know about the microbiota in the GI tract of horses, but the good news is, we know a lot more today than we did even five years ago. The more we know, the more our horses benefit.













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