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For her thesis, UD doctoral candidate 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.
For her thesis, UD doctoral candidate 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.

Inside the belly of the horse

Photos by Monica Moriak

Doctoral candidate Alexa Johnson goes inside the gut to investigate equine health

University of Delaware doctoral candidate Alexa Johnson grew up in California. She 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, the California native 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. “UD is within horse country — the equine mecca. The deep-rooted history and celebration of the horse and equine sport in this area helps the research find its footing.” 

Alexa came to UD for its research prowess, but she has full plate as a second-year graduate student. Like many, Johnson’s efforts have been altered by the coronavirus (COVID-19) pandemic, but Johnson normally teaches, manages labs and works with honors students in the Department of Animal and Food Sciences (ANFS). Johnson also serves as president of the ANFS Graduate Student Organization.

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.

Doctoral candidate 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.
Doctoral candidate 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.

However, Johnson wanted to take her research to a deeper level, specifically into the microbiome, which is the root of maintaining equine health and longevity. The microbiome encapsulates the extremely diverse range of microorganisms, genomes and interactions in the gastrointestinal tract of animals, including humans.

Horses are one of the most important animals in human history — strong enough to pull a heavy cart and agile enough to jump a six-foot fence. But, on the inside, their digestive systems are very sensitive to changes, stress or diet. You wouldn’t consider a belly ache a life-threatening event — unless you’re a horse. A constant conversation takes place between the gut microbes and the host and when that conversation becomes disrupted or agitated this can induce a myriad of gastrointestinal complications like colic.

While common and temporary occurrence for human babies, the disease is 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 UD 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. 

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

For her thesis, Alexa 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 said. “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,” Johnson said.

Doctoral candidate 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. This photo was taken before the coronavirus (COVID-19) pandemic prompted social distancing and restrictions on laboratory research.
Doctoral candidate 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. This photo was taken before the coronavirus (COVID-19) pandemic prompted social distancing and restrictions on laboratory research.

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.

Soon after Johnson joined the Biddle Lab, Jose Daniel Chazi Capelo and Usha Vyas were added to the doctoral stable. They’re busy at work on the Equine Microbiome Project, collecting samples from all over the country to build a library of bacterial DNA. 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,” said 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. 

UD’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. An indefinite list of research questions is possible with one horse’s sample.

Biddle values Johnson’s impact on the project. 

“Alexa is conscientious, focused, passionate, organized, inventive, curious, analytical and empathic,” said Biddle, who leads UD’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 (ANFS426) 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 (ANFS265), 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 said. “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 UD and that’s because I have a great working relationship with Dr. Biddle,” Johnson said. “She and I work well together on both a professional and personal level.”

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