Fecal Microbiomes of Feral and Domestic Horses Compared

Understanding the differences between these groups’ microbiomes and adjusting dietary and management practices accordingly could help improve domestic horse welfare.
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The NCSU researchers found Firmicutes bacteria were the most abundant microbe in a feral population of horses at Shackleford Banks, in North Carolina, while Bacteroidetes were more predominantly found in domesticated horses; this reflects the populations’ dietary differences. | Getty Images
Horses are hindgut fermenters, meaning they break down complex dietary fiber in the cecum and large intestine. This portion of the digestive tract houses most of a horse’s microbes, which through fermentation help produce vitamins as well as energy to meet a portion of the horse’s daily requirements. Despite the importance of that resident microbial community, known as the hindgut microbiome, scientists know little about it. Past research has shown that diet, age, exercise, disease, colic, medications, and whether a horse is domesticated affect the microbial population in a horse’s gut, said Cassandra Gluck, a PhD student at North Carolina State University (NCSU) in Raleigh, during her presentation at the 2023 Equine Science Society’s Symposium, held June 6-9 in Grapevine, Texas.

Gluck and her advisor, Shannon Pratt-Phillips, MSc, PhD, designed a study with the objective of assessing microbial populations across feral and domesticated horses using the feral Shackleford Banks horses, research and teaching horses at NCSU’s Equine Educational Unit, and privately owned horses at a local boarding barn.

The feral horses lived on a barrier island in North Carolina’s Outer Banks, where their diet is typically sea oats and island grasses, and their water source is ponds found throughout the island. The Shackleford Banks is a part of the Cape Lookout National Seashore, and the feral horse herd is overseen by National Park Service manager Sue Stuska, EdD. The NCSU herd is used for a mixture of research and teaching and consumed cool-season mixed pasture and minimal hay and concentrates during the study, while the privately owned horses ate a variety of concentrates, hay, and minimal pasture. Both groups of domesticated horses remained in their typical work programs and daily routines.

“We used fecal void swabs to collect samples and collected them quickly from the ground so as to minimize contamination,” said Gluck. The researchers then sent the samples to Purina Animal Nutrition’s technical center to be stored at -80 C before further analysis.

Firmicutes were the most abundant type of microbe found in the feral population of horses, while Bacteroidetes were more predominantly found in the domesticated horses. “Bacteroidetes is responsible for breaking down plant cell carbohydrates like starch,” she explained to TheHorse.com, “thus, the results indicating that the domesticated horse’s microbiome reflects their typical diet containing more starch versus the feral population of horses.”

Take-Home Message

Gluck said more research into the differences between the two populations’ microbes is needed to understand their significance. Further research will help equine nutritionists and horse owners manage domesticated horses’ microbiomes more effectively—using updated feed formulations, for instance, so microbes are “fed” more efficiently through the diet—and ultimately improve these animals’ welfare, she added.


Written by:

Haylie Kerstetter, Digital Editor, holds a degree in equine studies with a concentration in communications and a minor in social media marketing. She is a Pennsylvania native and, as a horse owner herself, has a passion for helping owners provide the best care for their horses. When she is not writing or in the barn, she is spending time with her dog, Clementine.

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