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A symbiotic population of bacteria, protozoa, and fungi, collectively called the microbiome, exists within the horse’s hindgut, a length of intestine composed of the cecum and large colon. Through fermentation, these microbes convert the fiber found in plants into the energy used for everyday bodily processes. The health and vigor of these microbes serve as a direct reflection of the well-being of the horse. Because of this, the diverse population of the microbiome should be thought of as vital and never marginalized or considered as an afterthought.

The effectiveness of the hindgut microbiome depends largely on its unchanging milieu, one in which the pH remains stable and beneficial bacteria outnumber pathogens or disease-causing bacteria. Any significant disruption in the microbial ecosystem, a condition known as dysbiosis, can affect the normal metabolism of carbohydrates, volatile fatty acids, and bile acids, ultimately resulting in enhanced water secretion, reduced water absorption, and diarrhea. Further, dysbiosis allows pathogenic microbes, such as Clostridium difficile, Clostridium perfringens, and Salmonella spp., to proliferate, potentially priming the hindgut for other problems.

While diet has a profound effect on the microbiome of the hindgut, other management decisions can also bring about dysbiosis and related problems.

Antibiotic therapy is a cornerstone of veterinary medicine, decreasing infection rates, recovery time from infections, loss of performance, and mortality. Common side effects of antibiotics, however, are well known and include reduced feed intake, allergic reactions, and diarrhea. Another major side effect is antibiotic resistance, a phenomenon in which bacteria that were once sensitive to an antibiotic become resistant to its action. Many classes of antibiotics can induce diarrhea, including tetracyclines, cephalosporins, fluoroquinolones, trimethoprim-sulfonamides, metronidazole, and several others. Multiple scenarios involving individual and combination therapies underlying the disease have been described in veterinary journals.

Called antibiotic-associated diarrhea, clinical signs range from mild to severe and may be sufficient to cause death, especially in hospitalized horses. Clinical signs are ill-defined in the veterinary literature regarding manure characteristics and frequency of defecation. The exact mechanism and scope by which antibiotics induce diarrhea in horses is speculative, but researchers believe that antibiotics alter the diversity of the microbiome, eventually leading to dysbiosis.

Diagnosis is typically based on the presence of diarrhea of unexplained origin except that it is associated in time with administration or cessation of antibiotics. A direct causal link between the antibiotic and the occurrence of diarrhea can rarely be made. Diarrhea can begin as soon as 24 hours after starting antibiotics or up to 8 weeks after stopping them. For horse owners, this can be financially draining, as antibiotic-associated diarrhea prolongs hospital stays and increases treatment costs.

One confounding aspect of antibiotic-associated diarrhea in horses remains: why some horses experience no ill effects during or after antibiotic treatment and others show severe clinical signs. In one review study, the incidence of antibiotic-associated diarrhea in horses varied from 3-52% in mature horses with diarrhea.

Because most horses must be treated with antibiotics at some point in their lives, keeping the hindgut healthy as a matter of course behooves horse owners. How can horse owners achieve this? Following these tenets of feeding management lays the foundation for hindgut health, even in the face of antibiotic use.

  • Horses rely on a forage-based diet to supply many of the calories necessary to grow, perform, and reproduce. Horses fed forage-based diets typically have a rich and diverse microbiome, suggesting resilience of the hindgut against disease-causing organisms.
  • In many instances, athletic horses cannot consume sufficient calories to sustain both optimal performance and moderate body condition. Offering concentrated sources of energy in the form of cereal grains or commercial mixes fills the gap between energy requirements and the energy available from forages.
  • Feeding large, high-starch concentrate meals may be problematic as starch can overwhelm the small intestine and flow into the hindgut before being digested entirely. The hindgut processes starch much differently than the small intestine does and, in doing so, the microbiome undergoes detrimental changes resulting from or leading to a drop in pH, known also as hindgut acidosis. Feeding small meals of no more than 0.5% of body weight per meal, e.g., 5 lb (2.5 kg) for a 1,100-lb (500-kg) horse, will help keep this in check, as will feeding low-starch concentrates that are designed to supply energy through alternative energy sources, primarily through fat (oil, sunflower seeds, or rice bran) and highly fermentable fiber (beet pulp or soy hulls). An ideal concentrate meal for a horse on antibiotics would contain no more than 1 g starch/kg body weight.
  • When high levels of concentrates are necessary to support athletic endeavors and body condition, as is often the case with racehorses and other elite performance horses, supplementary support of the hindgut may be necessary. This is doubly important if horses are also subjected to antibiotic therapy. In these instances, a hindgut buffer is warranted. The most effective hindgut buffer, EquiShure, features time-released technology that allows the buffering agent to remain protected until it reaches the hindgut. There, the buffering agent is released and acts to raise pH to a level that supports beneficial microbes.
  • Aside from those subjected to antibiotic therapy and those fed high-starch concentrates to fuel elite performance, other horses can benefit from a hindgut buffer. Transitioning seasons often dictate a change in forage quality available to grazing animals. A flush of green pasture in spring, for example, will often cause horses to have a change in manure consistency. The strategic use of a time-released hindgut buffer can counteract some of these changes.
  • Avoid long-term use of oral antibiotics for “preventative” purposes, including virginiamycin, to prevent pasture-associated laminitis.
  • Apart from cases of neonatal diarrhea in foals, there is little evidence to support the use of probiotics in preventing hindgut disturbances when horses are on antibiotics. If a horse has antibiotic-associated diarrhea, the most effective therapy may be fecal microbiome transplant, known also as transfaunation.

Owning horses is often an exercise in tending wounds and fussing over injuries, wrapping legs and worrying about all the things out of your control. The use of antibiotics at some point during a horse’s life is nearly inevitable. Even healthy horses are prescribed antibiotics occasionally to ward off infection from wounds, routine surgeries such as castration, or procedures involving diseased teeth or hooves. Horse owners should not be afraid to use antibiotics when prescribed by a veterinarian, but overuse must be discouraged to reduce the development of further antibiotic resistance and to protect the horse’s microbiome. From a feeding management perspective, help protect the hindgut from potential disruption by feeding free-choice forage, low-starch meals, and EquiShure, a research-proven time-released buffer.


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