Using fecal microbiota transplantation to improve gut health

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Fecal microbiota transplantation (FMT) is a technique used in humans primarily to treat Clostridium difficile infection. FMT uses healthy donor feces to modify the recipient’s gut microbial ecosystem to confer a health benefit. This technique is beginning to gain traction in the veterinary world with companion animals. This is usually a well-tolerated, minimally invasive process that can help improve a pet's gut microbiome.^1,2

Multiple factors go into the process of collecting and preparing for FMT. The first step is selecting and screening a donor. There are several screening recommendations that include, but are not limited to, being clinically healthy, having no history of current or chronic gastrointestinal (GI) signs, being at least 12 months old and younger than 75% of expected lifespan, and passing infectious diseases and microbiome screenings. Once a donor is selected, naturally voided feces from the donor are stored at –80 ℃ until they can be processed.¹

The processing steps can include multiple rounds of centrifugation and filtration before the material is lyophilized (freeze-dried) into a powder that can be encapsulated. Once the FMT is encapsulated, it can be used for various GI diseases, including parvovirus enteritis, chronic inflammatory enteropathy, canine acute idiopathic diarrhea, and other disease states still under investigation. FMTs can be administered rectally or orally, depending on the indication. Donor screening and dosing can be modified on a case-by-case basis to tailor to the recipient's needs.¹

Although most animal studies for FMT have had limited population sizes, investigators have seen promising results in the treatment of felines and canines. Future research is necessary to explore how the microbial variability from FMTs impacts the recipient's microbiome and clinical outcomes across multiple disease states. The Companion Animal FMT Consortium is a group of veterinary experts paving the way for more research into FMT. It has developed the first clinical guidelines for FMT preparation in companion animals. With a standardized process to obtain and process fecal matter properly, many of our furry companions can receive treatment for various GI-related conditions through FMT.²

Samantha Gorski is a 2025 PharmD candidate studying veterinary pharmacy at the University of Connecticut in Storrs.

References

1. Winston J, Suchodolski JS, Gaschen F, Verocai GG, Werner M. Clinical guidelines for fecal microbiota transplantation in companion animals. Advances in Small Animal Care. 2024;5(1),79-107. doi:10.1016/j.yasa.2024.06.006
2. Randolph NK, Salerno M, Klein H, Diaz-Campos D, van Balen JC, Winston JA. Preparation of fecal microbiota transplantation products for companion animals. PLoS One. 2025;20(4):e0319161. doi:10.1371/journal.pone.0319161