Written by: Shannon Pratt-Phillips, PhD

Your horse’s health depends greatly on the health of microscopic organisms that reside in his gastrointestinal tract.

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Disruptions to the microbial population can lead to a variety of ailments. While researchers work to understand this largely uncharted territory, you can help keep your horse in good health by feeding a carefully balanced diet.

As herbivores, horses consume plants, but they can’t actually process all the fibrous materials they ingest on their own. They require the assistance of intestinal microbes in order to digest such fibres, but little is known about these organisms. As such, researchers are on an ongoing quest to understand the microbial ecosystem better and discover how to maintain healthy populations in horses.

The Equine Digestive Tract

The rigid nature of plants is due in large part to the fibrous materials found in the cell wall that surrounds the cellular membrane. These fibrous materials include structural carbohydrates, such as cellulose, hemicellulose, pectin and lignin. Mammalian enzymes are not capable of digesting these fibres and, therefore, all herbivores must form a symbiotic relationship with microbial organisms within their gastrointestinal tract to assist in breaking down plant material into usable products. Microbes ferment carbohydrates (cellulose, hemicellulose, pectin and starch) into short chain fatty acids (SCFA), also called volatile fatty acids (VFA), which can be used by the host animal for energy production.

Dietary strategies differ across herbivorous species, in large part due to differences in their microbial ecosystems. Horses and cattle, for example, differ based on the structure of their digestive tracts and where their microbial populations reside. Horses are considered hindgut fermenters, meaning that the majority of their microbial population is located within their hindgut (cecum and colon). In contrast, ruminants, such as cattle, are considered foregut fermenters, where the majority of the microbial population exists in the multi-chambered stomachs (rumens) of these animals.

In horses, the major population of microbes resides in the large intestine (including the cecum, large colon, small colon and rectum). These intestinal compartments account for 64 per cent of the volume (about 100L) of the digestive tract, and digesta remains within this segment for between 24-48 hours to facilitate ample time for fermentation. A smaller population of microbial organisms resides in the stomach.

Typically, the microbial organisms ferment plant cell wall material, such as found in forages like hay or pasture grasses, into the SCFA (namely acetate, propionate and butyrate), which are absorbed by the horse and used for energy. Microbes also have the ability to ferment other non-structural carbohydrates such as starches, (found primarily in cereal grains) which results in the production of the aforementioned SCFA, but also lactic acid. Excessive lactic acid production (lactic acidosis) is believed to be a major culprit in many equine digestive disorders and some forms of laminitis.

The microbial organisms can also synthesize protein, but the extent to which microbial protein is available to the horse is unknown. Microbes are also important for their role in producing many of the vitamins required by the horse, including several of the B vitamins and vitamin K.

The microbial population of the horse is, therefore, of great importance, but it also presents a challenge. The microbial ecosystem is relatively fragile, and disruptions to the ecosystem due to diet or disease can result in significant health conditions including colic and laminitis. Despite the role of these organisms in overall equine health, relatively little is known about the equine intestinal microflora.

Identifying the Intestinal Microflora

The microbial population of the horse includes bacteria, protozoa, fungi and viruses. Over time, researchers have attempted to quantify the numbers of these microbes in different sections of the intestines, as well as to identify the individual species present. Studies have also aimed to determine how such populations change with diet and disease. As technology has improved, the methodology and techniques for such assays have become more advanced, including the ability to determine the genetic makeup of the microbial organisms, termed the “microbiome.” The microbiome refers to the entire genetic makeup (genome) of all of the microbial organsisms associated living inside the body. The human microbiome project is a major initiative to investigate and understand the microbial organisms living within people. Similarly, work is underway to better understand the microbes living within horses.

Dr. Scott Weese, DVM, DVSc, Dipl ACVIM, a Professor of Pathobiology at the University of Guelph, conducts extensive research in the field of equine bacterial populations. He pointed out that ‘there are probably 10 times the number of bacterial cells in a horse compared to horse cells,’ to highlight the vastness of the microbial population. Bacterial cultures (in which populations of bacteria are grown in petri dishes) have provided some early numbers of bacterial populations in different parts of the intestine.

Bacterial populations range from 4.3 x 108/gram (430 million bacteria per gram) in the stomach, 2.9 x 106/gram in the duodenum (first part of the small intestine), 1.26 x 109/gram in the colon and 2.05 x 109 in the cecum. It should be noted that while information generated from bacterial cultures can be useful, it may not tell the whole story, as only bacterial cultures that will grow on the culture media are represented. It is likely, therefore, that these numbers represent a major underestimation and that there are billions upon billions of bacteria in each gram of intestinal content.

Other studies identify bacteria based on their function within the different regions of the digestive tract. For example, some microbes are cellulolytic (meaning they break down cellulose), hemicellulolytic (break down hemicellulose), or amylolytic (break down starch to lactic acid; often referred to as lactic acid producers), while other bacteria are lactate utilizers.

More recent studies, including those performed at the University of Guelph by Dr. Weese and Dr. Marcio Costa, use DNA sequences to identify the taxonomic classification of the microbes within the feces of horses (this classification includes the domain, kingdom, phylum, class, order, family, genus and finally species, of all living things). Their studies and others have found that equine bacterial populations are highly diverse (the number of different species), and while horse-to-horse variation exists, many of the key populations appear to be conserved within horses.

Specifically in healthy horses, the highest number of bacteria are found within the phylum Firmicutes, with other significant numbers in the phyla Bacteroidetes, Proteobacteria and fewer numbers of the phyla Fibrobacteres, Verrucomicrobia, Fusobacteria, Actinobacteria and Spirochaetes. Significant numbers of bacteria within the order Lactobacillales, Clostridiales and Fibrobacterales are found in horses. Key genera include Fibrobacter spp., Ruminococcus spp., Streptococcus spp. and Lactobacillus spp. Interestingly, research from Dr. Weese at Guelph found that Clostridium difficile, which is normally considered a pathogenic species, is commonly found in healthy horses. Further, while clostridia bacteria are often considered to be harmful components on the intestinal microflora, clostridia are actually very common inhealthy horses and a population of many harmless clostridial species may be important for horse health.

Intestinal Microflora and Disease

It is likely that the microbial population within a horse is relatively stable, but disruptions to the ecosystem, either through diet, antimicrobial therapy or other disease, can have profound impacts on the health of the horse.

Colic, or digestive upset, is a condition that may be caused by a multitude of factors, one of which may be explained by a disruption to the microbial ecosystem. Increases in gas production (a byproduct of fermentation) may result in gas colic. Similarly, excessive lactic acid production (lactic acidosis), alters hindgut pHs, changing the integrity of the intestinal lining. This may result in colitis (inflammation of the colon) and/or the absorption of toxins (endotoxins or vasoactive amines released by microbes in response to changes in pH) potentially resulting in laminitis. Furthermore, the shift in pH inhibits some species of bacteria (primarily cellulolytic bacteria) and favours lactic acid-producing bacteria, thereby exacerbating the problem.

It is well-established that carbohydrate overload (in the form of grain), or more recently oligofructose (from lush pastures or frosted grass, for example, fructan) overload, can trigger laminitis, likely as a result of altering the microbial population in the hindgut and triggering the cascade of events as described above. The key microbial species that are involved in this chain reaction are only now being identified, however. Research out of The University of Queensland in Australia has examined cecal and fecalbacteria in horses following laminitis induction through the administration of oligofructose. It was determined that lactic acid-producing bacteria of the Streptococcus bovis/equinus complex proliferated following oligofructose administration and at the onset of laminitis development. Research isstill required to determine how these bacteria, and potential acidosis, results in the inflammation of the laminae of the hoof.

Dr. Weese and colleagues from the University of Guelph aimed to identify differences in microbial populations in healthy horses, and those with undifferentiated acute colitis (meaning the exact cause of the colitis was unknown). Using DNA sequencing, these researchers determined that there were profound differences in the microflora between the two groups. The predominant phyla of healthy horses were the Firmicutes (68 per cent), followed by Bacteroidetes (14 per cent) and Proteiobacteria (10 per cent), while in horses with colitis, themajor phylum was Bacteoidetes (40 per cent), followed by Firmicutes (30 per cent) and Proteobacteira (18 per cent). The authors suggested that the vast differences at such a high taxonomic level (phylum) may indicate that shifts in the entire microbiome is involved in disease pathogenesis, rather than one bacterial species, and that colitis should be considered a disease of the intestinal bacterial population, not just relating to growth of a specific bacterium (e.g. Salmonella).

As mentioned earlier, the stomach also has a small population of microbial organisms, and this population has been implicated in playing a role in the development of gastric ulcers. When horses are fed high starch diets, the microbes within the stomach, which is rich in lactic acid-producing bacteria, can ferment these simple carbohydrates to produce lactic acid. When coupled with the stomach’s hydrochloric acid, it can be damaging to the mucosal lining of the stomach resulting in ulceration. Dr. Weese pointed out that the development of ulcers in horses is “in contrast with humans, where H. pylori infection is associated with ulcers.”

A further consideration, and complication, regarding the intestinal microflora is with respect to antimicrobial therapy. There are often times where a horse requires antimicrobial therapy for systemic disease, and the veterinarian needs to outweigh the risks of various drugs on the disease itself versus the potential negative effects on the microflora. When microbial drugs, such as antibiotics, are administered to horses, they may not be absorbed in their entirety, thus resulting in some drug remaining as it reaches the large intestine. Here, the drug may also act on the microbes of the intestine, thus altering normal digestion and fermentation. In addition, the drug may result in the overgrowth of pathogenic bacteria, which may result in colitis or other antibiotic-associated diarrhea.

Intestinal Microflora and Diet

The horse’s digestive tract and intestinal microflora are well-suited to the pasture-dense diet which horses evolved on. Today’s horses, however, have heightened nutritional needs, primarily energy, and, as such, their diets often consist of concentrated energy sources such as starch-rich grains. Furthermore, today’s pastures have been developed for cattle, and may be less suited to our horses.

High intakes of grain and other highly digestible carbohydrate sources are associated with an increased risk of colic. Colic is likely a result of a shift in microbial fermentation, causing an increase in lactic acid and gas production. Epidemiological research of colic risk factors suggests that feeding more than five pounds of grain per day significantly increases the risk of colic.

Several studies have shown that horses appear to have an upper limit to small intestinal starch digestion, wherein if they are fed increased amounts of starch (greater than three grams/kg body weight), more starch bypasses the small intestine and reaches the large intestine where it can be fermented by cecal and colonic bacteria. Research has shown that high starch diets decrease pH in the cecum, colon and feces. Further, it has been shown that when horses are adapted to higher grain diets, their microbial profile shifts to have larger numbers of bacteria, more lactobacilli and streptococci, and lower pH.

Similarly, when there is a sudden change to the diet (grain or hay), it may cause disruption to the microbial ecosystem, as evidenced by the fact that changes in diet (changes in a batch of forage, or changes/introduction of grain) are also a risk factor for colic. Abrupt introductions of grain to the diet has been shown to cause changes to the microflora, such as increased bacterial counts and increased lactic acid production, in as little as five hours. Introduction of haylage or silage, however, has fewer effects on the microbial ecosystem.

Related work by the author, Dr. Pratt-Phillips, and her colleagues at North Carolina State University, has found that accelerated pasture intakes associated with restricted grazing results in lower pH compared to horses at pasture for 24 hours (who likely eat slower and have less of an overload of carbohydrate-rich pasture). Similarly, horses at pasture overnight (turned out when plant non-structural carbohydrate content was the highest) have lower fecal pH than horses turned out either during the day, or those with continuous access to pasture. While individual bacteria were not examined in these studies, it is clear that diet plays a role in microbial fermentation, potentially contributing to disease risk.

Prebiotics and Probiotics

Knowing that a healthy microbial population generally results in a healthier horse, it is of great interest to determine if the microflora can benefit from supplementation. Probiotics are live microorganisms that exert a positive effect to the host and are often referred to as direct-fed microbials. Probiotics are often bacteria that are already present in the gut (such as Lactobacillus spp). Prebiotics are compounds that positively affect the existing microflora, either through affecting the composition or activity of the microbes.

Extensive work has been conducted in humans and horses, and despite some promise for human conditions, work in horses does not appear to show much benefit from probiotic supplementation. In fact, one study by Dr. Weese reported that Lactobacillus pentosus WE7, a promising probiotic for the prevention of foal diarrhea, was associated with an increase in diarrhea. Work from the University of Maryland showed that direct-fed microbials did not reduce the risk of acidosis when horses were fed high-starch diets. In contrast, some yeasts have been shown to be beneficial when given to horses with colitis (decreased severity and duration of disease), and may improve fibre digestibility. Dr. Weese said that it may ‘be a matter of balance, not more is better,’ when it comes to probiotic supplementation, highlighting the need to better understand the normal balance of gut flora.

Owners should be cautioned, however, when it comes to selecting probiotics. Dr. Weese published a study highlighting the lack of regulations when it comes to labels for probiotics. In fact, only 27 per cent of the products that made claims regarding organisms actually met those claims.

There has been little work conducted on prebiotics in horses. Thus far the research is intriguing, however. Work from France not only found that supplementation with small amounts of fructo-oligosaccharides reduced disruptions to the microflora following a sudden diet change, but also appeared to improve insulin sensitivity in horses. The mechanisms for these benefits are unknown thus far, but warrant further research.

Future Direction

With improvements in technology, it is becoming easier to distinctly identify bacterial and other microbial species within the equine digestive tract. It is likely that such research will identify differences in the microflora across the different segments of the digestive tract, between healthy and diseased animals, and potentially among healthy animals of different breeds or types. From there, we can expand our work to include the effects of probiotic and prebiotic supplements, the effects of different dietary management strategies, and to determine methods to attenuate the onset of acidosis. The work of several universities across the globe, including the groundbreaking research from Dr. Weese and his team from the University of Guelph, are beginning to understand the complexity of the microflora of a normal and healthy horse.