The Equine Microbiota by Body System

Discover what researchers are learning about the microbiota’s role in the horse’s digestive system, respiratory tract, skin, and more.

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Researchers have found the equine stomach microbiome to be abundant, diverse, and different from one horse to another. | iStock

What researchers are learning about the microbiota’s role in the equine digestive system, respiratory tract, skin, eyes, hooves, and more

The hundreds of trillions of organisms living inside and on our horses’ bodies play major roles in their health. The horse’s best-known ecosystem of microbes, known as a microbiome, is that of the gut, which is responsible for aiding digestion and might also influence functions such as breathing, learning, and performing. But beyond that, microscopic communities inhabit and influence every bodily system, says Marcio Costa, PhD, of the Department of Veterinary Biomedical Sciences at the University of Montreal, in Quebec, Canada.

In 2008 the National Institutes of Health initiated the Human Microbiome Project (HMP), developing a microbiome databank based on samples from 300 healthy people. Recognizing the importance of microbiota throughout the body, scientists investigated microbiomes in people’s gastrointestinal tracts, on their skin, and in their mouths, noses, and reproductive tracts.

While there’s no comparable equine project, scientists are taking advantage of more advanced and less expensive genetic sequencing technology to explore the microbiomes of equids, Costa says. In this article we’ve selected seven systems and parts attracting the attention of equine scientists aiming to unravel how these microscopic communities affect our horses’ health, welfare, and more.

1. The Digestive System

The GI tract starts with the mouth, but studying the mouth’s microbiome is complicated by the fact that horses eat, drink, and lick ­frequently—constantly picking up microorganisms from the environment, says Costa. Even so, several research groups have associated the microbiome of the gums, teeth, and mouth with various dental diseases, discovering pathogenic strains of bacteria.

Cornell University researchers first studied the microbiome of the equine stomach in 2012, finding it abundant, diverse, and different from one horse to another. In most subsequent studies of the gastric microbiome, scientists investigated its possible link with gastric ulcers or ulcer treatment but found only mild associations. By contrast, German researchers discovered Jerusalem artichoke meal supplementation led to a dramatic increase in equine stomach microbiota diversity.

A few teams—including Costa’s—have mapped out the microbiota of healthy horses and donkeys from the stomach to the feces, finding significant differences in composition and diversity depending on the gastrointestinal region.

The most deeply investigated microbiome in horses is the one in their hindgut (the GI tract beyond the small intestine), Costa says, which scientists now know is usually predominated by two bacterial phyla: Bacteroidetes and Firmicutes. The next-most-common phylum is generally Proteobacteria, followed by Verrucomicrobia, Fibrobacteres, and/or Actinobacteria.

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Disruptions in the healthy gut microbiome might affect pH levels and how the digestive system breaks plants down, Costa explains. Researchers at the University of Pennsylvania are looking into links between the gut microbiome and colic.

Costa’s team, meanwhile, has picked up “very subtle, very specific small changes” in the gut microbiomes of asthmatic horses compared to healthy ones—­especially when switching between stalls with dry and moldy hay and pasture. “These weren’t drastic changes like you’d see with colitis or diarrhea,” Costa says. “And it doesn’t mean the gut microbiome is causing the disease.”

Rather, it suggests lung inflammation affects other body parts, confirming long-held theories about what scientists call “the gut-lung axis,” says Costa’s colleague, Mathilde Leclère, PhD, who led the study: “The idea that the gut microbiota influences systemic inflammation is not new.”

The gut microbiota might also affect mental processes such as learning and behavior. With abundant nerves and neurons linking the digestive system to the nervous system, “there’s constant communication between the brain and the gut,” says Costa. “That’s why people say our gut is our second brain. And it’s why we say we have ‘gut feelings.’ ”

That could also explain why horses produce loose feces when they’re stressed, he adds. Researchers are already investigating links between the human gut microbiome and depression, anxiety, and other mental disorders, as well as any clinical effects of prebiotics and probiotics.

In horses, preliminary study results have shown some associations between the gut microbiome and behavior. But Costa cautions against drawing conclusions too early. “These are just associations,” he says.

2. The Respiratory Tract

Researchers studying humans consider the microbiome of the upper and lower respiratory tracts the “gatekeeper to respiratory health.” Renaud Léguillette, DVM, MSc, PhD, Dipl. ACVIM, ACVSMR, and his team at the University of Calgary in Alberta, Canada, first sequenced it in horses in 2017.

They found that Proteobacteria was the most abundant phylum (44%) in healthy horse airways, followed by Firmicutes (17%), Bacteroidetes (13%), and Actinobacteria (22%). The lower airways weren’t as rich in microbes as the upper airways, he reports, with only minor differences in relative abundance.

As for asthmatic horses, the team found increased numbers of Streptococcus as well as significant differences in relative abundances in their lower airway microbiota, Léguillette says.

Three years later his team showed that corticosteroid treatments decreased microbial diversity in the equine nose and trachea, altering the relative abundance of eight bacterial genera but having no effect on fungi. A dusty environment appeared to alter the makeup of both bacterial and fungal populations significantly more than the treatments did.

That same year, Leclère and her colleagues found that asthmatic horses had lower tracheal bacterial loads than healthy horses, possibly due to the disease process, inflammation, or prior asthma treatments, she says.

It could even indicate the horses didn’t get enough exposure to germs in the environment as foals, making them more susceptible—a theory arising from studies in rodents, Costa adds.

Meanwhile, researchers at China’s Yangzhou University veterinary school reported in 2020 that donkeys’ nasal microbiomes became richer and more diverse immediately after a 21-hour road trip in an open-top truck. In particular, the scientists noted a relative increase in Proteobacteria and a relative decrease in Firmicutes, which they suspect might be part of a respiratory disease process.

In 2021 a team of researchers at Texas A&M University found significant differences in the upper respiratory microbiomes of healthy horses versus those with an inflammatory airway disease called nasopharyngeal cicatrix syndrome (NCS). One fungus in particular, Bipolaris, was also increased in healthy horses living on NCS-affected farms, leading to the possible identification of a culprit in this poorly understood disease.

Scientists at China Agricultural University, in Beijing, found significantly greater relative abundance of Proteobacteria and significantly less abundance of Firmicutes and Actinobacteria in donkeys carrying Streptococcus equi subsp. equi (S. equi), which causes strangles.

And in Ontario, Canada, researchers discovered that the noses of horses infected with equine herpesvirus type 1 (EHV-1) had higher relative abundance of Proteobacteria and lower abundances of Firmicutes and Bacteroidetes compared to healthy horses and, overall, they had less bacterial richness and diversity.

Even healthy horses have a lot of individual variation, warranting further research, says Scott Weese, DVM, DVSc, Dipl. ACVIM, of the University of Guelph.

3. The Skin

In 2018 Christine Theoret, PhD, DMV, Dipl. ACVS, at the University of Montreal, and her colleagues—including Costa—sequenced the skin microbiomes of three healthy horses. Their microbiomes were very similar and dominated by Acidobacteria, which is low in abundance on human and mouse skin.

That study also revealed a surprising amount of previously unknown bacteria that didn’t yet have a name at the genus level; 20% were even unknown at the phylum level. The findings not only underline the uniqueness of horse skin microbiota compared to other species but could also “truly reflect the presence of a high number of unknown bacteria in the skin of horses, which might be of special importance for the development of new therapies,” Theoret says.

The study also revealed that bandaging alters skin microbiota, Costa says, which could affect how wounds heal—including whether proud flesh (exuberant granulation tissue) or biofilms (barriers that make them difficult to treat topically) develop. “Maybe in the future we can identify specific bacteria associated with those types of complications,” he says.

Recently, Sarah Kaiser-Thom, DVM, PhD, an immunologist at University Hospital Heidelberg, in Germany, and her colleagues discovered that Staphylococcaceae families were much more prominent in the pasterns of horses affected by scratches, or equine pastern dermatitis, while three other families—­Sphingomonadaceae, Burkholderiaceae, and Microbacteriaceae—were significantly less prevalent. Staphylococcus might be outcompeting other species without necessarily causing the disease, she explains.

4. The Eye

In 2021 researchers at Texas A&M investigated the fungus-only ­microbiota—the mycobiota—of the eyes of 12 horses and discovered abundant types that had previously never been associated with horses’ eyes. They also noted that horses at pasture had greater varieties of fungus in their tear films, which might put them at greater risk of eye infections after an injury, the team reports.

In spring 2022 researchers at Chile’s Universidad Andrés Bello reported on the microbiomes of the eyes of 14 healthy horses. They identified 278 genera belonging to 17 phyla, with Proteobacteria representing 60%, followed by Actinomycetota (22%) and Bacteroidota (16%).

While these ocular microbiota findings are interesting, they don’t reveal what’s going on inside the eye, say researchers at China’s Sun Yat-sen University. Studies investigating the microorganisms inhabiting the inner eye structures—including the vitreous humor, which appears to be a favorable environment for ­microorganisms—could prove useful, they say.

5. The Reproductive Tract

Until 2019 humans, minipig sows, dairy cows, and ewes were the only mammals with published data on their reproductive system microbiomes. That year, Empar García-Roselló, PhD, at Cardenal Herrera-CEU University, in Spain, and her team published results on the vaginal microbiota of eight Arabian mares. They found the communities were dominated by Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria and, unlike women, contained very little Lactobacillus. Contrary to findings in other mammals, the microbiota were fairly stable throughout the reproductive cycle.

That doesn’t appear to be the case higher up in the tract, says Jenny L. Sones, DVM, PhD, Dipl. ACT, associate professor of theriogenology (animal reproduction) in Louisiana State University’s School of Veterinary Medicine, in Baton Rouge. Her DVM/PhD student Kalie Beckers recently determined the uterine microbiome is more diverse during estrus than anestrus. Beckers is analyzing data to determine how intrauterine antimicrobials affect the uterine microbiome and impact fertility.

In July 2022 Sones’ team was set to present more reproductive microbiome findings—including the extrauterine microbiome in the pregnant mare and how the stallion semen microbiome correlates with fertility—during the annual Therio Conference. Sones and fellow veterinary theriogenologists are founding a ­consortium to further investigate what they call “The Theriome.”

“There are observational studies that are leading us to believe that there is a link between the vaginal microbiome and fertility, or with the incidence of postpartum diseases like metritis, but … nobody has proved that so far,” says Costa.

6. The Urinary Tract

The urinary tract wasn’t part of the initial HMP because scientists believed urine was “sterile,” meaning it had no microbes. In 2012, however, scientists at Loyola University Chicago sequenced human urinary tract samples and discovered a broad range of microbes. This “unique commensal flora colonizing the urinary tract” apparently plays “an important role in global urological health,” says Tiago Antunes-Lopes, MD, PhD, of the University of Porto, in Portugal.

Researchers have since found evidence linking the urinary tract ­microbiome—the “urobiome”—to conditions in humans, including overactive bladder, urinary tract infections, and cancer.

Between 2017 and 2020 scientists sequenced the urobiomes of dogs and cats, but the equine urobiome has yet to appear in scientific publications. 

8. The Hoof

The equine foot is in constant contact with the ground, where it can pick up microbes that vary by region, ground surface, season, and climate, Costa says. Logically, horses must have a unique hoof microbiome that fluctuates according to the environment in which they live and changes in association with various hoof diseases, he says. That’s certainly the case for cattle, sheep, and elk, as researchers have recently revealed. Even so, they’ve yet to explore the horse hoof microbiome.

Take-Home Message

The microscopic worlds of the tiny organisms inhabiting our horses’ bodies are finally getting explored thanks to modern genetic sequencing technology. Those explorations don’t stop at the most popular microbiome—that of the gut. Scientists are studying microbiomes specific to individual body systems, from the head to the hooves, to not only comprehend their role but find therapies that support a healthy microbiome balance.


Written by:

Passionate about horses and science from the time she was riding her first Shetland Pony in Texas, Christa Lesté-Lasserre writes about scientific research that contributes to a better understanding of all equids. After undergrad studies in science, journalism, and literature, she received a master’s degree in creative writing. Now based in France, she aims to present the most fascinating aspect of equine science: the story it creates. Follow Lesté-Lasserre on Twitter @christalestelas.

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