Study questions added benefit of faecal microbiota transplantation for canine chronic enteropathy

22 June 2026

A new study has found no clear evidence that adjunctive faecal microbiota transplantation improves clinical outcomes in dogs with chronic enteropathy compared to dietary management alone.

While chronic enteropathy treatment that supports the microbiome is favoured over antibiotic therapy, the clinical benefit of faecal microbiota transplantation remains uncertain.

A new blinded, randomised control trial, published in the Journal of Small Animal Practice and led by the medicine team at Willows Veterinary Centre and Referral Service, explored whether the addition of faecal microbiota transplantation (FMT) could improve clinical outcomes in dogs with chronic enteropathy.

Researchers recruited 42 dogs from six UK referral centres, all presenting with small intestinal or mixed diarrhoea. Dogs were randomly assigned to receive either faecal microbiota transplantation and a dietary change (a hydrolysed or novel protein diet), or the standard treatment of a dietary change only. Faecal microbiota transplantation was performed using fresh faecal material from screened donor dogs, administered by a retention rectal enema under sedation.

Both groups of dogs showed progressive improvement over time in stool consistency, confirming the high rate of food responsiveness in canine chronic enteropathy. However, there were no significant differences between groups in owner-reported reported clinical improvement, Canine Inflammatory Bowel Disease Activity Index (CIBDAI) or faecal score after 90 days. No major adverse events attributable to FMT were reported during the study, suggesting that the procedure is safe.

Overall, the findings show that a single FMT administered via retention enema did not provide a clear clinical benefit over dietary change alone, although more research is required to evaluate repeat administration, extended course (e.g. via oral administration) or larger transplant volumes. Dietary trials remain first-line therapy for dogs with chronic enteropathy.

The study had several limitations, including not reaching the target sample size, the mild nature of most of the chronic enteropathy cases, and lack of consistency in diet changes and concurrent treatments.

Lead author, Dr Fergus Allerton, said: “The authors are proud to add some valuable data from this RCT to the literature around FMT. This field continues to advance rapidly with new findings reported frequently. The absence of clinical benefit in this study should not be interpreted as evidence of absence but, nonetheless, does highlight the need for rigorous studies to support novel therapies. More work with adjusted FMT protocols is warranted. We look forward to continuing to investigate ways to foster a healthy gastrointestinal microbiome.”

Read the study in the Journal of Small Animal Practice: https://onlinelibrary.wiley.com/doi/10.1111/jsap.70137