In Europe, there are approximately 180 million dogs and cats, and about 30 million of them suffer from chronic enteropathy. It is now scientifically proven that fecal microbiota transplantation (FMT) can represent a solution, or at least a meaningful support, to improve the quality of life of these animals.
Recently, we conducted a survey on FMT involving a sample of 200 veterinarians. It emerged that most of them, although aware of FMT, do not use it. When asked, “What is the main obstacle to adopting FMT in your clinical practice?”, the most common answer was: “I don’t know enough about it.”
We therefore felt it was important to help reduce these barriers. To this end, we provide a summary of the roundtable discussion that concluded one of the many valuable sessions of the Microbiome Forum organized by the Purina Institute, entitled Putting microbiome science into clinical practisewhich was held online on November 12–13, 2025.
A wide range of topics were addressed, from microbiome perturbations in early life stages to the gut–brain and gut–skin axes, from antibiotics as a risk factor to chronic enteropathy and fecal microbiota transplantation (FMT).
During the event, it was highlighted that approximately 15% of dogs suffer from chronic gastrointestinal disorders, and that around 80% of animals benefit from fecal microbiota transplantation. This percentage is consistent with what we observe at EuBiome when analyzing data from dogs and cats treated with lyophilized capsules.
Below are some of the most interesting questions on FMT raised by participants, along with the answers provided by the speakers: Prof. Stefan Unterer, Dr. Francesco Lotti, and Dr. Ana Rostaher.
1) Are there contraindications to FMT, for example in immunocompromised animals?
Answer:
Based on the reported clinical experience, no true contraindications to FMT have emerged, not even in immunocompromised animals. Unterer cited the example of puppies with severe intestinal barrier dysfunction and neutropenia, who showed better outcomes when treated with FMT compared to untreated controls.
The rationale is that the intestine is already densely populated: introducing functional microbiota does not increase risk but may instead promote ecosystem recovery.
2) How do owners react when FMT is proposed?
Answer:
Acceptance is generally good, especially when FMT is explained as an adjunct therapy within a multimodal approach. Owners are more receptive when they understand that the goal is to reduce the use of steroids and antibiotics.
In early-detected cases, FMT is often introduced as a second-line option after dietary intervention.
3) When is FMT used within the therapeutic pathway?
Answer:
FMT is not considered first-line therapy, but:
- it is introduced after dietary management
- it is part of long-term disease management
- it is repeated in cases of relapse or loss of remission
Unterer emphasized that in chronic diseases we speak of clinical remission rather than definitive cure, and that regular follow-up is essential.
4) Should FMT be repeated? According to which protocol?
Answer:Yes, in chronic cases:
- Lotti tends to perform two FMTs as a new induction; a third only if the response is incomplete
- Unterer repeats FMT at the reappearance of even mild symptoms, integrating it into follow-up
Both noted that some owners report general improvements (energy, overall well-being) and spontaneously request another administration.
5) What side effects have been observed?
Answer:
In dermatological patients (atopic dermatitis), FMT proved to be very well tolerated.
The only observed effects were:
- temporarily softer stools
- one single case of immediate expulsion of the material, requiring repetition
No cases required permanent discontinuation of treatment.
6) Do you have experience with oral FMT (capsules)?
Answer:
Lotti reported no direct experience with the oral route and mainly uses enema, considered simple and effective.
However, both acknowledged that evidence supports oral FMT, which may be particularly useful for maintaining remission when available.
7) Does FMT also work in cats?
Answer:
Yes, FMT can also work in cats, especially:
- in young animals
- after antibiotic exposure
In older cats or those with advanced disease, the response may be more variable.
8) Is FMT safe in puppies and kittens?
Answer:
Yes, particularly in cases of antibiotic-induced dysbiosis. Data from the “Growing Dog Project” show that the microbiota can return to a normal range as early as 10–12 weeks of age, making the use of adult donor FMT acceptable in selected cases.
9) Does FMT have a role in dermatological diseases?
Answer:
Yes. In dogs with atopic dermatitis, FMT:
- is well tolerated
- has shown no significant adverse effects
- fits within the gut–skin axis framework
It is viewed as an immunomodulatory tool within a multimodal approach.
Shared message from the FMT panel
FMT is a safe, flexible, and integrable clinical tool. It does not replace diet, nutrition, or inflammation control, but acts on the intestinal ecosystem that supports all these functions.
Il mio messaggio
Anyone interested in deepening their knowledge of the microbiome in small animals will find in the event Putting microbiome science into clinical practise moltissime informazioni utili, così come in tutti altri gli eventi del Microbiome forum.
La rivoluzione è in corso e non si può ostacolare.
Lasciati trasportare e fai buon viaggio!
Barbara Simionati
She holds a degree in Biology and a Master in Business and Management (MBM). She worked for many years in the field of DNA sequencing and later in microbiome research. She is co-founder of two spin-offs of the University of Padua: BMR Genomics and EuBiome. She currently serves as CEO of EuBiome and as Adjunct Lecturer at the Department of Pharmaceutical Sciences of the University of Padua.
