What makes a horse an easy keeper? The gut microbiome comes under scrutiny

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Alexa Johnson is investigating the microbiomes of easy, medium and hard keeper horses. While easy keepers can live on relatively little food, hard keepers can be prone to be too thin with difficulty maintaining adequate weight. Photo: Monica Moriak

The microorganisms that populate a horse’s gut are crucial to their health, and essential for the digestion of their fiber-rich diet.

Changes in the make-up of these gut microorganisms have been linked to serious problems, including colic and laminitis.

However, far less is known about how differences in this extremely diverse range of microorganisms in the gastrointestinal tract, which scientists call the microbiome, affects the ability of horses to put on and hold weight.

For her thesis, University of Delaware doctoral candidate Alexa Johnson is investigating the microbiomes of easy, medium and hard keeper horses.

“If you think of these terms as a human analogy, easy keepers are those people who gain ten pounds by just ‘looking’ at a McDonald’s spread,” Johnson says.

“Hard keepers are those people who eat McDonald’s for breakfast, lunch and dinner and won’t gain a single pound.”

Those same characteristics can be seen in horses, which makes managing these animals difficult.

“I want to know how the equine microbiome community structure and functionality compare between the easy keeper and the hard keeper, how is the microbiome associated and can we manipulate it.”

Identifying the microbiome differences associated with health and disease is a necessary first step to designing therapies or interventions to restore balance and function to the digestive system of colicky horses as well as the horses who struggle to maintain a healthy body weight.

Alexa Johnson is busy at work on the Equine Microbiome Project, collecting samples from all over the country to build a library of bacterial DNA. Photo: Monica Moriak

Johnson, who grew up in California, stayed in her home state to earn her bachelor’s and master’s degrees.

But, when it came time for her doctorate, as an equine researcher studying health and disease, she knew she had to move across the country.

“I knew that, to do equine nutrition, I needed to come to the east coast, where horse research happens on a larger scale,” Johnson said.

During her own time as an undergraduate, Johnson studied animal science at the University of California, Davis, with an equine science emphasis. She stayed there for a master’s in animal biology to pursue her passion for equine nutrition and conducting horse feeding trials.

However, Johnson wanted to take her research to a deeper level, specifically into the microbiome.

While outwardly, horses are tough and strong, their digestive systems are very sensitive to changes, stress or diet. Disruptions can induce myriad gastrointestinal complications such as colic.

While gut upsets are a common and temporary occurrence for human babies, they are a leading cause of death for horses.

Gastrointestinal diseases are a serious matter and the gut microbiome is the leading culprit. These chronic issues create management challenges for horse owners and veterinarians.

Identifying the microbiome differences associated with health and disease is a necessary first step to designing therapies and interventions.

When looking for doctoral programs, Alexa discovered that University of Delaware equine science researchers were investigating what role bacteria play in maintaining a healthy gut.

After reading research papers from Amy Biddle, assistant professor of animal science, Johnson cold-called her. Previously, Biddle had master’s students, but none at the doctoral level.

Alexa Johnson, right, and her adviser Amy Biddle, assistant professor of animal science, are collecting samples from horses of all ages, breeds, disciplines and management styles to identify the core microbiome of a horse. The photo was taken before the coronavirus pandemic prompted social distancing and restrictions on laboratory research. Photo: Monica Moriak

“I told Dr. Biddle that I enjoyed her work and asked if she was accepting Ph.D. students,” Johnson explains.

Soon after, Johnson joined Biddle’s lab. Jose Daniel Chazi Capelo and Usha Vyas were added to the doctoral stable.

They are busy at work on the Equine Microbiome Project, collecting samples from all over the country to build a library of bacterial DNA.

Samples from horses of all ages, breeds, disciplines and management styles are collected to identify the core microbiome of a horse.

“The power of the Equine Microbiome Project is the large number of samples it contains,” says Johnson, who is pursuing her doctorate in Animal and Food Sciences.

“A limiting factor to any study is a small sample number. With the rolling admission of equine microbiome samples, we have amassed more than 200 samples to be used in our studies.”

In addition to the difficulty of finding research with large groups of horses, these studies may not reflect the level of horse care in the average horse barn. Therefore, the results may not be applicable to the average horse.

The university’s sampling kits have gone everywhere from Massachusetts and Virginia to Oregon and California, with a waiting list of people who are interested in submitting.

The university’s equine sample library is designed for reuse.

Biddle values Johnson’s impact on the project.

“Alexa is conscientious, focused, passionate, organized, inventive, curious, analytical and empathic,” says Biddle, who leads the university’s Equine Microbiome Research Laboratory.

“As a Ph.D. student, she has established collaborations across campus and is fearless in trying new techniques or thinking in new ways. She can accomplish more in 24 hours than most people can do in a week.”

Outside of her research pursuits, Johnson leads Equine Management lab sessions, where students apply scientific principles of nutrition, healthcare, behavior and reproduction to horse management. She is also a teaching assistant for Perspectives in Career and Professional Development, which emphasizes career discovery and development in animal and food sciences.

“As a teacher and mentor for undergraduates, she is clear and articulate, and a natural leader,” Biddle says. “She can inspire confidence and respect and hold students to a high standard. At the same time, she has a keen sense of humor and fun.”

For aspiring students, Johnson stresses the key to graduate school is building a strong connection with your adviser.

“I’ve really enjoyed my time at the University of Delaware and that’s because I have a great working relationship with Dr. Biddle,” Johnson says. “She and I work well together on both a professional and personal level.”

Reporting: Dante LaPenta

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