Fecal microbiota transplantation (FMT) has demonstrated clinical benefit across multiple canine gastrointestinal conditions, with the strongest evidence in chronic enteropathy (CE) and parvoviral infection, and emerging data in acute hemorrhagic diarrhea syndrome (AHDS).

In dogs with CE, repeated or single rectal FMT consistently reduces disease activity scores. A single rectal FMT reduced the canine chronic enteropathy clinical activity index (CCECAI) from a median of 8 (range 5–14) at baseline to a median of 3 (range 1–12) at day 7 and a median of 1 (range 0–12) at day 30, with an average response duration of approximately 10 weeks.Journal of Vete… In a separate cohort of 20 CE dogs treated with 1–2 rectal FMTs, the canine inflammatory bowel disease activity index (CIBDAI) fell from a median of 5 (range 1–9) at baseline to a median of 1 (range 0–5) at 1 month and 1 (range 0–3) at 3 months, with 10 of 17 dogs with follow-up data remaining clinically stable at 6–12 months.Journal of the… In a larger retrospective series of 41 CE dogs treated with 1–5 rectal FMTs (median 3), 31 dogs responded, with CIBDAI falling from a median of 6 (range 2–17) to a median of 2 (range 1–9).Journal of the… Dogs with less severe dysbiosis at baseline had longer-lasting responses than short-term responders or non-responders.Journal of the…

Baseline dysbiosis index predicts FMT response in CE dogs. Dogs with a long-lasting response — defined as clinically stable for more than 12 weeks — had significantly less marked dysbiosis at baseline compared to short-term responders or non-responders.Journal of the… This mirrors findings in human ulcerative colitis, where patients responding to FMT had less depletion of core microbiota than non-responders.Journal of the…

In parvoviral infection, FMT as an adjunct to standard care shortens hospitalization and accelerates diarrhea resolution. Among survivors, FMT combined with standard treatment (intravenous fluids and antimicrobials) produced a median hospitalization time of 3 days versus 6 days with standard treatment alone.Journal of Vete… Mortality was 21.2% in the FMT group versus 36.4% in the standard treatment group, though this difference did not reach statistical significance.Journal of Vete…

In AHDS, FMT does not provide additional benefit over symptomatic treatment alone in short-term recovery. No significant differences in clinical course were found between dogs treated with FMT plus symptomatic treatment versus symptomatic treatment alone, and no antibiotic regimen was superior to standard treatment with or without FMT in reducing Clostridium perfringens strains.Journal of the… All dogs showed rapid clinical improvement regardless of treatment group.Journal of the…

In chronic large bowel diarrhea, a single rectal FMT produces faster initial CIBDAI improvement but equivalent 30-day outcomes compared to psyllium husk. The FMT group showed more rapid onset of CIBDAI improvement, but no differences were observed in fecal scores, defecation frequency, or time to recurrence of diarrhea episodes at 30 days; the FMT group did show greater improvement in bodyweight and body condition score at 30 days.Veterinary Reco…

FMT has also been used successfully for refractory Clostridium perfringens diarrhea, with fecal character normalizing in all 8 dogs treated by rectal enema and 6 of 8 dogs testing negative for C. perfringens alpha toxin gene expression post-FMT.Journal of Vete…

The rectal enema route is safe in dogs, with no serious adverse events reported in healthy recipients. Mild adverse events were observed in some dogs but could not be definitively attributed to FMT in the absence of a placebo group; dogs with pre-existing comorbidities may experience a different adverse event profile than healthy dogs.Journal of Vete… No FMT-related complications occurred in a separate cohort of dogs with idiopathic persistent diarrhea, and 71% demonstrated improved fecal parameters post-FMT.Frontiers in Ve…

A critical limitation across CE studies is that clinical improvement does not consistently correlate with microbiota changes. Recipient microbiota composition and diversity did not change significantly over time despite clinical improvement in one CE cohort, and significant variation in donor microbiota composition was observed across different donations.Journal of Vete… Glycerol (10%) as a cryopreservative was associated with a significant difference in microbiota composition compared to samples stored without it.Journal of Vete…

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