The Equine Microbiota by Body System

What researchers are learning about the microbiota’s role in the equine digestive system, respiratory tract, skin, eyes, hooves, and more

The hundreds of trillions of organisms living inside and on our horses’ bodies play major roles in their health. The horse’s best-known ecosystem of microbes, known as a microbiome, is that of the gut, which is responsible for aiding digestion and might also influence functions such as breathing, learning, and performing. But beyond that, microscopic communities inhabit and influence every bodily system, says Marcio Costa, PhD, of the Department of Veterinary Biomedical Sciences at the University of Montreal, in Quebec, Canada.

In 2008 the National Institutes of Health initiated the Human Microbiome Project (HMP), developing a microbiome databank based on samples from 300 healthy people. Recognizing the importance of microbiota throughout the body, scientists investigated microbiomes in people’s gastrointestinal tracts, on their skin, and in their mouths, noses, and reproductive tracts.

While there’s no comparable equine project, scientists are taking advantage of more advanced and less expensive genetic sequencing technology to explore the microbiomes of equids, Costa says. In this article we’ve selected seven systems and parts attracting the attention of equine scientists aiming to unravel how these microscopic communities affect our horses’ health, welfare, and more.

1. The Digestive System

The GI tract starts with the mouth, but studying the mouth’s microbiome is complicated by the fact that horses eat, drink, and lick ­frequently—constantly picking up microorganisms from the environment, says Costa. Even so, several research groups have associated the microbiome of the gums, teeth, and mouth with various dental diseases, discovering pathogenic strains of bacteria.

Cornell University researchers first studied the microbiome of the equine stomach in 2012, finding it abundant, diverse, and different from one horse to another. In most subsequent studies of the gastric microbiome, scientists investigated its possible link with gastric ulcers or ulcer treatment but found only mild associations. By contrast, German researchers discovered Jerusalem artichoke meal supplementation led to a dramatic increase in equine stomach microbiota diversity.

A few teams—including Costa’s—have mapped out the microbiota of healthy horses and donkeys from the stomach to the feces, finding significant differences in composition and diversity depending on the gastrointestinal region.

The most deeply investigated microbiome in horses is the one in their hindgut (the GI tract beyond the small intestine), Costa says, which scientists now know is usually predominated by two bacterial phyla: Bacteroidetes and Firmicutes. The next-most-common phylum is generally Proteobacteria, followed by Verrucomicrobia, Fibrobacteres, and/or Actinobacteria.

Disruptions in the healthy gut microbiome might affect pH levels and how the digestive system breaks plants down, Costa explains. Researchers at the University of Pennsylvania are looking into links between the gut microbiome and