The microbiota of any animal refers to the collection of micro-organisms, such as bacteria, viruses, protozoa, and yeast that reside on or in the body of that animal. These microbial inhabitants are not invaders but beneficial colonizers. They participate in numerous critical functions such as nutrient assimilation, and immune response support. Trillions of these microbes inhabit each animal, most of them residing in the gut, particularly the large intestine. For herbivores, these communities specialize in the fermentation of dietary fiber, providing the body with energy substrates.
Like other herbivores, horses too have a unique and diverse microbiota. Of particular importance for adequate nutrition, strength, stamina, energy, development, and immunity of the horse, are the microbial communities that inhabit their digestive tracts starting with the esophagus, stomach, small intestine, large intestine, and finally the rectum. Several factors such as age, diet, genetics, and environmental factors such as the stress experienced during training, and travel to competitions, influence the microbial diversity found in the horse gut.
In contrast to ruminants such as cattle, goats and sheep, the horse is a hindgut fermenter, meaning that the large intestine is the site of fermentation of ingested fiber. The hindgut, which includes the cecum and the colon, can hold up to 32 gallons of fibrous feed material as it ferments for several days. Being a hindgut fermenter is a huge advantage to horses because it essentially gives them a second chance to process energy from the feed that has already passed through the small intestine. While the horse’s microbiota found throughout the gastrointestinal tract plays an important role in overall health, the hindgut is most significant. Here the microbiota works to break down food so the horse can absorb the nutrients and provide for its daily energy needs.
Within their gastrointestinal tract, horses are known to host up to 1015 bacterial cells with the majority of bacteria residing in the colon, especially within the comparatively enlarged caecum. Recent research has focused on unveiling the composition of the equine hindgut “core” microbiota. Although early findings indicated that there is no “standard” microbiota in horses that is shared across the species, some general patterns have emerged. Distinct microbial communities are observed in each major compartment of the equine gut i.e. the upper gut (stomach, jejunum, and ileum) and the lower gut (cecum and the colon). Microbial composition between neighboring compartments of the horse’s gut is more similar compared to that observed in distant locations along the gastrointestinal tract. Also, the upper gut microbiota is fairly varied due to the variation in environmental bacteria that are present in the horses’ forage. The microbiota of non-domesticated horses is more diverse compared to that of domesticated horses.
Researchers have been able to define certain “key microbes” that typically inhabit the horse’s gut. Firmicutes and Bacteroidetes represent the largest classes of the equine intestinal bacterial community ranging from 40% up to 90% in different compartments. Certain other cellulolytic species are also integral to the equine hindgut as they play a critical role in degrading the plant cell wall. The second largest group of microbes found in the horse’s gut are Proteobacteria. They play an important role in nitrogen fixation and are largely found in the upper gut, particularly in the ileum. The third important group of microbes found in the equine gut are what are called Verrucomicrobia. They are primarily found in the equine caecum, small colon, and rectum. Several lactic acid bacteria such as Lactobacillus reuteri and L. bulgaricus are also common residents of the equine gut. All these different classes of micro-organisms help maintain a healthy equine gut ecosystem which is responsible for various functions such as fermenting fiber in the hindgut and boosting the horse’s immune system.
