The horse’s gastrointestinal (GI) tract houses a vast community of microbes, with distinct populations in different regions. This complex ecosystem is difficult to study yet sits at the center of digestive health—possibly even diseases such as gastric ulcers.

The Equine Microbiome

The term microbiome can refer to any microbial community in or on the body. “We’re most commonly talking about the (hind)gut microbiome, but there’s a skin microbiome, an ocular microbiome, etc., so, the term ‘microbiome’ is the overarching community, which includes bacteria, (fungi), and sometimes also viruses that live in that area,” says Rebecca Bishop, DVM, MS, PhD, Dipl. ACVS (LA), a lecturer in the Department of Veterinary Clinical Medicine at the University of Illinois, in Urbana.

The equine gastrointestinal microbiome includes all the microorganisms that live in the GI tract, says Aaron Ericsson, DVM, PhD, associate professor of pathobiology and integrative biomedical sciences and director of the Metagenomics Center at the University of Missouri, in Columbia. “The bulk of that biomass is bacterial organisms, so that gets the most interest in research and, arguably, the bacterial populations residing in the equine gut probably have the greatest impact on host health,” he adds.

Gastric Ulcers in Horses

Gastric ulcers affect a large population of horses, and researchers are exploring whether the stomach microbiome contributes to ulcer development.

Equine gastric ulcer syndrome (EGUS) describes ulceration in either the squamous (upper) or glandular (lower) stomach. “The horse’s stomach is unique in that it has two different portions, even though it is a single chamber,” explains Bishop. “The squamous portion is most like the lining of our esophagus, and then the glandular portion is what is comparable to our stomachs, where there are glands that secrete acid, mucus, and other components.”

From this anatomy veterinarians classify ulcers as squamous gastric disease (ESGD) or equine glandular gastric disease (EGGD). “The two diseases have different underlying causes and risk factors, so even though we group them together (as EGUS), they are quite different from each other,” Bishop says.

Equine Microbiome Research

A horse’s GI tract spans about 100 feet and the microbial communities vary widely. “The upper GI tract and the stomach in particular are completely different,” says Ericsson. There’s a bit of overlap—you’ll see some taxa (group of living organisms) across all regions—but generally they’re very different.

Sampling the microbiota in the stomach is somewhat easier than in structures deeper in the GI tract.

“Typically, the groups that I have worked with in this field are doing (stomach) biopsies and collecting a couple of samples when they are doing the scope procedure,” Ericsson says. “They’ll take that little chunk of tissue and bring it to the lab to extract DNA and … figure out all of the bacteria that are present on those biopsy samples.” This data collection is the beginning of building large-scale datasets. Through understanding the bacteria that are present both in horses that have gastric disease, and those that do not, researchers might be able to identify patterns when more data is available.

“I would say that we don’t know if the microbiome plays a role in the disease process for gastric ulcers,” says Bishop. “As the field of research has evolved, and the better we get at DNA sequencing, the more we find and the more information we have, the more complicated it gets. However, we do know that the microbial communities change in disease states, and that they also change in response to environmental factors such as diet and exercise.”

Additionally, says Ericsson, “in a couple of the studies that I have helped with, (we) have identified subtle differences between control horses and populations with gastric disease.”

“One of the things that research has pretty consistently found is that lactate-producing and fibrolytic bacteria seem to be more populous in healthy states,” adds Bishop. “So, whether that’s because those bacteria are beneficial, or because they’re more likely to get damaged when the system is upset, we don’t know whether it’s a cause or an effect.” If the lactate-producing and fibrolytic bacteria are more populous in healthy horses, it could mean that they are more likely to be damaged when disease is present because research has shown that there are less of these bacteria types in horses that have gastric ulcers.

Unanswered Questions and Future Research

Researchers still have many unanswered questions about the stomach microbiome’s potential role in gastric health. “Most of our research thus far has looked at what are the species, genus, or families present,” says Bishop. “And because we started with DNA sequencing to say what is there, we’re starting to think that it is probably not so much who it is, but what they do (that) is more important.”

The current evidence shows microbial communities differ in health and disease, but their connection to gastric ulcers has yet to be defined.