Treating Diarrhea in Horses: Frozen Fecal Microbial Transplantation

Fecal microbial transplantation (FMT) can, though unconventional, be used for treating diarrheic horses with dysbiosis. Having frozen samples ready to use eliminates some logistical issues surrounding FMT but may not prove efficient.

The rationale for FMT is to transfer the fecal microbiome from a healthy donor horse to a recipient with an unbeneficial shift in the intestinal microbiome, a condition known as dysbiosis. Fecal slurries are administered into the stomach to recipient horses using fresh or frozen samples.

Studies in humans, however, show that exposure to freezing temperatures and oxygen decreases bacterial viability. To determine the effect of freezing, oxygen, and cryoprotectants on the viability of the bacteria in fecal samples, veterinary researchers collected feces from 10 healthy horses. Those samples were processed either in an anaerobic chamber or in room air and preserved with either 10% glycerol or a cryoprotectant containing nutrients and antioxidants. All samples were frozen at -20° C for 90 days. Samples were then thawed to measure bacterial viability.^*

Researchers noted three primary findings:

• Freezing decreased bacterial viability in the fecal samples by almost 50%;
• Samples preserved with glycerol had higher viability compared to samples preserved with the cryoprotectant; and
• Exposure to air did not significantly affect viability.

 “This substantial decrease in viability following freezing and thawing of fecal samples is a concern, because bacteria viability of FMT is believed to decrease during transit through the stomach and small intestine. The fewer live bacteria that reach the large intestine, the less effective this procedure will be,” explained Catherine Whitehouse, M.S., a Kentucky Equine Research nutrition advisor.

Added to this, about 40% of the bacteria in freshly collected fecal samples were nonviable. This represents the bacteria that may have passed from more proximal portions of the intestinal tract. Thus, finding ways to maximize viability of bacteria in donor fecal samples is essential. Based on this study, fresh fecal samples are preferable to frozen samples, which is not nearly as convenient.

The large intestinal microbiome can be quite sensitive to changes in diet, management, medications, and even exercise. Dysbiosis readily occurs in horses, potentially leading to diarrhea, and often accompanied by acidic shifts in hindgut pH due to the change in microbial population.

“To support horses during times of dysbiosis and acidosis, providing a hindgut buffer such as EquiShure may help neutralize excess acid and support the hindgut microbiome,” advised Whitehouse.

EquiShure is a time-released buffer that uses patented encapsulation technology to target release of the buffer directly into the hindgut to restore an appropriate pH and maximize digestive health.

 ^*Arantes, J.A., R. Di Pietro, M. Ratté, L.G. Arryo, M. Leclère, and M.C. Costa. 2025. Changes in bacterial viability after preparation and storage of fecal microbiota transplantation solution using equine feces. PeerJ 13:e18860.