How Diet Affects Equine Gut Health

Discover what scientists are learning about this dynamic area of research and how we can use it to promote equine health.

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How Diet Affects Equine Gut Health
The type of forage horses eat matters to the microbiota—both in the way microorganisms break it down and how it affects hindgut microbial composition. | Photo: iStock

What we’re learning about this dynamic area of research and how we can use it to promote equine health 

Blue colicked in his stall so violently, the farm’s vet in Baltimore, Maryland, immediately arranged transport to a referral hospital. The 10-year-old off-track Thoroughbred went down in the trailer several times before arriving at New Bolton Center, in Kennett Square, Pennsylvania. There, he underwent successful surgery for large colon volvulus.

“We thought he’d be on his way back home within the week,” recalls his owner, Karin de Francis. “But then, the odyssey started.”

Blue colicked again several days after surgery but responded to pain medications. A week later he colicked again. Then again, and again. Despite diet changes, anti-ulcer medications, and pain management, Blue continued to show intermittent signs of mild colic. His veterinarians couldn’t find anything on ultrasound or X ray. Even his intestinal biopsies were normal, leaving his caretakers frustrated about how to help.

“He kept having these repeat, medicaltype colics that didn’t need surgery,” says Alicia Long, DVM, emergency and critical care fellow at New Bolton. “And when we did some digging into his history—back to his life on the track—we learned that he was known for being ‘ulcery.’ ” Blue never got scoped for ulcers, though, and his bouts of lying down and not wanting to eat might have been from colic instead.

At New Bolton, Blue journeyed in and out of colic episodes for the next 10 months, finally going home healthy in July 2021. As the gray gelding’s gut oscillated between stable and chaotic, on the outside scientists worldwide were delving into the guts of humans and horses alike, using the latest genetic sequencing technology to better understand the vast and mysterious world of the microbiome. With more than 8,000 peer-reviewed papers published on the gut microbiome while Blue was hospitalized, including dozens specifically on horses, the scientific world was exploding with new information about these microscopic communities inhabiting the digestive tract.

In a way, Blue’s timing was perfect. His case inspired the New Bolton team to explore the possible links between the gut microbiome, diet, and recurrent colic.

What’s particularly exciting, Long says, is it could lead to a hands-on fix for owners. “Diet is something we can do, something we can change,” she says. “If you can change dietary management, then theoretically you could potentially help reduce risk of colic—and that’s really the white whale in equine research right now.”

The New Bolton team, including Blue’s surgeon, Louise Southwood, BSc (Vet), Dipl. ACVS, ACVECC, has joined the international push to unveil the microbiome’s secrets, with potentially revolutionary ways to manage horses’ digestive health. In this article we’ll review what scientists are learning.

The Microbiome: A Hot Topic

The gut microbiome’s prevalence in today’s research world has much to do with advancing technology, says Simon Daniels, PhD, senior lecturer of equine management and science at the Royal Agricultural University, in Cirencester, U.K.

Powerful genomic sequencing is available at a fraction of what it cost a decade ago, he says. That means researchers can more easily run DNA sequencing on the microscopic communities inside the digestive tract. Microbiome research, however, is still very much in its infancy, he adds. Scientists are mostly collecting data on the bacterial community profiles they find in the gut in different situations: In horses, that means healthy or sick, stabled or pastured, forage-only diets vs. complementary feeds, etc.

“We know that food goes in, and energy comes out, but nobody’s ever fully understood what happens or why,” Daniels says. “We still don’t know what a ‘normal’ microbiome looks like, and we don’t know the functions of the different (microorganisms). And if we don’t know the full function, that doesn’t tell us the full story.”

Two things we do know. One: “When we make changes (to the microbiome), changes occur—possibly with negative health consequences,” he says. Two: “Horses are quite variable. We don’t always know what’s normal for all horses, but we might find out what’s normal for an individual horse.”

Equine nutritionist Anna Garber, PhD, of the School of Veterinary Medicine at the University of Glasgow, in Scotland, recently reviewed more than 150 studies of the equine gut microbiome. She noted it’s hard to isolate the different factors influencing the gut microbiome, and labeling bacteria as “good” or “bad” isn’t the right approach. Gut health seems to be more dependent on delicate balances and context, she says.

Even so, a few generalities appear to be emerging.

“What we have so far really gives us a powerful tool to start understanding how that black box of the hindgut functions,” Daniels says. “That gives us a much better idea of what we can do to improve the diet—and hence the health and welfare—of horses, and that’s where this gets really exciting.”

Bacteroidetes and Firmicutes: Fighting for the Top?

Thousands of bacterial species can live inside your horse’s gut. Bacteria are categorized according to groups, from general to more specific: Domain / Phylum / Class / Order / Family / Genus / Species.

In the equine gut, scientists usually find two bacterial phyla that predominate: Bacteroidetes and Firmicutes.

Bacteroidetes are Gram-negative bacteria—meaning they have a tough outer membrane that makes them more resistant. They break down cellulose and pectin in plant cell walls, helping horses digest forage. Within the Bacteroidetes phyla, researchers often refer more specifically to the genus YRC22, among others.

Firmicutes, on the other hand, produce short-chain volatile fatty acids (VFA), which give horses energy. Within the Firmicutes phyla, equine researchers often mention the Clostridia class, the Clostridiales order, and the Ruminococcaceae and Lachnospiraceae families.

The Bacteroidetes and Firmicutes phyla appear to switch out as the most dominant phylum in the microbiome. What difference the Bacteroidetes-to-Firmicutes ratio makes is still unclear, Garber says.

The phylum that usually comes in third is Proteobacteria, a Gram-negative bacteria group that includes potential pathogens, such as Salmonella and Escherichia, which in a healthy horse’s gut might be part of a healthy mix, our sources say.

Other, less-common phyla, including Verrucomicrobia, Fibrobacteres, and Actinobacteria, also break down plants.

In general, scientists believe a greater diversity of species means a healthier gut environment, says Daniels.

Bacteria’s Links to pH

Two common families of the energy- producing Firmicutes phylum in horses’ guts, Lactobacillus and Streptococcus, release lactic acid as a byproduct. Certain levels of lactic acid production can be useful, contributing to an appropriate pH balance—essentially neutral, at about 7— in the digestive system, says Daniels.

But an overabundance of either Lactobacillus or Streptococcus could make the environment too acidic for some kinds of fiber-degrading bacteria, “which would die off,” he says.

Acidic environments also make it harder for certain Firmicutes families to survive—in particular, Lachnospiraceae, which produce the valuable VFA butyrate. Butyrate not only provides energy but also helps maintain the health of the colon’s epithelial cells. This contributes to intestinal wall integrity, which can prevent leaky gut, says Long.

Reductions in gut pH might also lead to acidosis, diarrhea, and colic, says Garber.

How Diet Affects Equine Gut Health
Blue’s veterinarians at New Bolton Center (pictured) are waiting on analyses results to understand how his microbiome evolved during his stay. | Photo: Courtesy Karin de Francis

Forage: Type Matters

The type of forage horses eat matters to the microbiota—both in the way microorganisms break it down and how it affects hindgut microbial composition. “It’s critical to understand how the forage itself alters this sensitive ecosystem,” says James Lattimer, MS, PhD, assistant professor of equine nutrition at Kansas State University, in Manhattan.

Lattimer’s recent study in six cecally cannulated Quarter Horses showed they had lower cecal pH (more acidic) but an increased abundance of Streptococcus, Lactobacillus, and YRC22 when consuming an alfalfa hay diet versus brome hay. They also had more VFA-producing Firmicutes, giving the horses more energy, he says.

In New Zealand, scientists found pastured horses’ microbiomes changed ac- cording to season. During pasture growth periods, Firmicutes dominated but, when pasture was dry, Bacteroidetes took over. Regardless of season, pasture-fed horses had more diverse fecal microbiomes than hay-fed horses, the researchers say.

Forage has its own microbiome— which Daniels calls the “haybiome”—that might get transferred into horses’ guts at mealtime. In his recent study Daniels found that dry meadow hay is generally abundant in bacteria that help digest plants. These bacteria were surprisingly resistant to high-temperature hay-steaming processes, which killed off disease-causing pathogens in the hay.

Researchers in China recently compared horses’ fecal microbiomes when fed pasture grass, hay, or haylage and found lower amounts of Streptococcaceae-family bacteria in horses on pasture grass than those on stored forage. They also saw more Lachnospiraceae-family bacteria in the guts of hay-fed vs. haylage-fed horses.

Concentrates: Disrupting the pH Balance

One of the main issues with concentrated feeds is they contain starches that can ferment in the hindgut, causing the pH to become more acidic, says Daniels.

Texas A&M University researchers, working with six cannulated horses, saw significant drops in cecal pH within 12 hours of feeding concentrated feeds and free-choice hay. Over the next seven days those levels hovered just above, and occasionally dropped under, a pH of 6—a critical threshold indicative of hindgut acidosis, which can cause anorexia, colic, and laminitis.

The researchers also noted that when the horses consumed concentrates, they had significant reductions in Fibrobacteres and Clostridiales, whereas YRC22 concentrations increased.

Probiotics and Prebiotics

Knowing horses need certain types of bacteria in their microbiomes, wouldn’t it make sense to give them in a supplement?

That’s the idea behind probiotics, which are oral powders, pastes, and liquids containing certain species of “helpful” microorganisms, and prebiotics, which are the fiber sources for the microbiota to break down, or “food” for the probiotics, Daniels says.

In theory, these should help stabilize horses’ gut microbiota, he says. In reality, research is lacking—and conflicting. Worse, labels don’t always accurately reflect what’s in the product, Long says. Probiotics and prebiotics do seem to influence the microbiome, at least temporarily, but it’s not clear to what extent those changes are beneficial.

Daniels offers several possible explanations: Oral supplementation means the microorganisms must survive the acidic passage through the stomach to get into the hindgut, and we don’t have proof they do. If they do get there, they don’t seem to colonize, making any effects short-lived.

Still, probiotics appear safe for adult horses, and some manufacturers add them directly into their feeds in hopes of improving digestibility. “If you can potentially improve fiber degradability or reduce the harmful effects of starch, then that’s not a bad thing,” Daniels says.

Take-Home Message

While Blue is better, his vets at New Bolton still don’t have all the answers, and they’re waiting on analyses results to understand how his microbiome evolved during his stay. But Blue may be a poster child for how diet, the equine gut microbiome, and digestive health intertwine. As scientists learn more about the millions of microorganisms inhabiting horses’ digestive systems, we stand to gain critical knowledge about feeding that microbiome to promote optimal health and welfare.


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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