What can the microbes living inside your horse’s gut say about the current state of his health? A recent study by researchers at the University of Missouri suggests there’s quite a lot to learn. But sampling these bacteria is no easy feat.

Traditionally, the only microbes researchers could study were those residing in the large intestine or found in fecal matter. But they believed that analyzing harder-to-reach microbes—those living in the stomach, small intestine, and cecum—might yield more information.

“The luminal bacteria are the focus of most microbiome studies wherein fecal samples are collected,” said Aaron Ericsson, DVM, PhD, a research assistant professor in the University of Missouri’s Department of Veterinary Pathobiology. “We wanted to determine if the populations of bacteria in intimate contact with the epithelium (tissues lining the gastrointestinal tract) were distinct from the luminal populations.”

To that end, a team of researchers set out to generate a detailed DNA profile of healthy gastrointestinal tract (GIT) bacteria from nine adult horses euthanized for reasons unrelated to metabolic or intestinal disease. The team sampled microbes found in both food particles and feces (luminal), as well as microbes attached to the mucous lining the GIT’s walls (mucosal), taking care to collect samples from similar locations between horses.

Upon completing the DNA profiles, the researchers found luminal bacteria from the stomach and small intestine (upper GIT) “highly variable” between horses, whereas bacteria from the cecum and large intestine (lower GIT) were “remarkably similar between horses.” Their findings suggest microbes in the lower GIT regions are fairly stable and less affected by differences that occur higher in the GIT.

They found that the mucosal bacteria appeared more uniform than the luminal bacteria throughout the length of the entire GIT.

So what can horse owners take from these findings?

“I think the take-home message is simply that there is an unbelievably dynamic and complex ecosystem at work inside the horse’s gut,” said Ericsson. “These horses were from different parts of mid-Missouri, were of different ages and breeds, and had very different life stories. Personally, I think this speaks to how closely equine health is tied to gut (microbial) health.”

Ericsson also relayed that ongoing and future research will explore the differences in the microbial populations between healthy horses and those affected by various conditions.

“The ultimate goal is to identify disease biomarkers in the gut microbiota that can then be used as diagnostic or prognostic indicators,” he said.

The study, “A Microbiological Map of the Healthy Equine Gastrointestinal Tract,” was published in PLoS One.