Fecal Microbiota Transplant (FMT)

A Fecal Microbiota Transplant (FMT)

Fecal Microbiota Transplant (FMT) is a well-established treatment approach that has been used effectively in both humans and animals. An FMT is the transfer of stool, which contains healthy functioning microbes and the byproducts of fermentation, from a healthy donor to the gastrointestinal (GI) tract of an ill recipient. That transfer can be done in clinic (via colonoscopy, retention enema, or endoscopy) or with enteric-protected oral capsules. The diverse and well-functioning community of microbes from the donor material take up residence in the recipient’s gut.

By providing a complete set of native healthy, species-specific gut microbes, FMT can resolve a variety of symptoms associated with imbalance or dysbiosis of the gut microbiome—including digestive disorders like inflammatory bowel disease (IBD), skin problems like atopic dermatitis, and various immune system issues.1–4

FMT is the best known approach for restoring balance in a gut microbiome and has proven to be an effective treatment in both humans and companion animals.5,6

The History of FMT Use in Humans

FMT has been used in human medicine for thousands of years. The transfer of fecal material from a healthy   to a diseased person to cure disease goes back as far as fourth-century China, and has been performed for hundreds of years throughout Europe. The practice gained momentum in the United States in the 1950s and has become an increasingly widespread treatment method with well-documented success.

The nonprofit OpenBiome has the world’s largest stool bank for humans, and one of the organization’s main objectives is to expand safe access to FMT. (The OpenBiome website includes a handy video about how FMT works.)

The Food and Drug Administration (FDA) approves the use of FMT for some human health conditions, although the procedure continues to demonstrate beneficial results for many conditions that are not yet approved.

For example, FMT is an FDA-approved treatment of Clostridium difficile (C. diff) infections. And it has proven to be the most promising solution for the low gut bacterial diversity associated with Crohn’s disease (a form of IBD).7 FMT has also been used successfully in clinical trials to reduce inflammatory events in people with multiple sclerosis (MS) and to treat the symptoms of autism.8,9 Another study demonstrated that FMT can be used to stop the progression of type 1 diabetes in humans.10

FMT Use in Animals

FMT has been used in large-animal veterinary medicine since the 17th century.11 In cattle and horses, the practice is often called “transfaunation.”12 Since the mid-20th century, FMT’s success against C. diff infections in humans has led to an expansion of this approach into small-animal veterinary medicine, especially as a treatment for chronic diarrhea in cats and dogs.6

Many animal studies have shown that FMT can help resolve diarrhea caused by inflammatory bowel disease (IBD) or parvovirus (parvo), as well as skin issues like atopic dermatitis.3,5,13

In a study conducted by AnimalBiome, 72 cats and 40 dogs with IBD were given a 25-day course of oral FMT capsules (our Gut Restore Supplement). Symptoms improved in 83% of the cats and 80% of the dogs. About a quarter of the cats and half of the dogs also had an increase in appetite. This study demonstrates that even though FMT can’t always cure IBD, it can be an effective tool to improve symptoms and increase quality of life for pets.

How FMT is Administered

FMT can be delivered in the clinic via colonoscopy, retention enema, or endoscopy, or orally via enteric protected capsules. AnimalBiome has developed its one-of-a-kind fecal transplant in an oral capsule, offering a convenient and safe approach to fecal transplantation for cats and dogs.

AnimalBiome’s FMT Gut Restore Supplement is an oral FMT with an enteric coated capsule that gives your patient the benefits of FMT without the need for surgery or sedation. Our FMT Gut Restore Oral Supplement delivers native healthy core microbes from species-specific screened donor stool. Our donor material is highly screened for pathogens and parasites, cross referenced with our healthy reference set, cryoprotected, and freeze-dried. Stable at room temperature, the capsules offer a noninvasive, and an affordable alternative for your patients suffering from microbiome dysbiosis associated issues.

For patients that are pill-defensive or who have severe dysbiosis, we offer species-specific enema material from our rigorously screened donors. Learn more about our donor screening process.

Symptoms or Conditions That FMT Can Help With

Extensive scientific evidence already supports the effectiveness of FMT for a number of conditions and diseases, and as research continues into the connections between microbiome imbalances and health conditions, more ways that FMT therapy can benefit overall health are sure to be revealed.

In cats and dogs, FMT has proven to be especially useful for the two categories of health problems that account for the majority of visits to veterinarians: digestive and skin conditions.14

Digestive Conditions

Clinical symptoms related to the digestive system can have different causes and present in a variety of ways, such as diarrhea, constipation, vomiting, regurgitation and weight loss. When dealing with refractory cases or those where other more common diagnoses have been ruled out, checking the gut microbiome should be the next step in the diagnostic plan. A gut microbiome test can show an imbalance within the microbiome due to missing bacteria or overgrowths of pathogenic microbes.

For example, the genus Escherichia can be a beneficial member of the community when it makes up only a small part of a cat’s or dog’s gut microbiome. But an overgrowth of Escherichia can cause diarrhea and other clinical digestive symptoms. Elevated Escherichia levels are very common in cats and dogs.

FMT can resolve diarrhea quickly by introducing a diverse community of beneficial bacteria that out-compete the harmful microbes, restoring healthy function to the digestive system.

Skin Conditions

Research has shown that chronic or recurring skin conditions—such as edema, atopic dermatitis, hair loss, and recurrent ear infections—have a connection to the gut microbiome. Skin conditions are often caused by a defective immune system response, and most of the body’s immune cells live in the GI tract.2,4,15–17 In addition to interfering with proper immune function, an imbalanced gut microbiome can cause the intestinal walls to become more permeable, or “leaky” (a factor that is often associated with food allergies).

Both of these effects—a compromised immune system and a leaky gut—can manifest as skin disorders. A dysfunctional gut environment is also more prone to inflammation, which can trigger hyperactive immune responses all over the body and cause common clinical symptoms like pruritus, redness, and dermatitis associated with skin disorders.

Read more about atopic dermatitis and the gut microbiome:

How FMT Works

By replenishing your patient’s microbiome with all the right bacteria in the right proportions, FMT capsules can reestablish balance and resolve symptoms. While outcomes vary, positive results—such as better-formed stool, improved appetite, and decreased pruritus—are often seen within a few weeks. In patients with severe gut microbiome imbalances, it may take longer to see improvement. Depending on a patient’s age and underlying health conditions, the process of establishing the newly introduced microbial populations can sometimes take two or three months.

The FMT Gut Restore Supplement provides native healthy species-specific microbes. The capsule’s enteric coating prevents it from dissolving until it reaches the intestines, where the contents seed your patient’s gut with a diverse array of healthy bacteria and restore any missing groups.

If your patient’s Gut Health Test report shows an overgrowth of pathogenic bacteria, FMT capsules can help remove these bacteria through competitive exclusion. If your patient’s overgrowth is due to E. coli, we recommend a full course of our GI Relief Supplement concomitantly to maximize the benefits of the Gut Restore Supplement.

Learn More About How to Improve Your Patient’s Gut Health

FMT Safety In Pets

Our Gut Restore Supplements are an effective, noninvasive approach that provides the benefits of a fecal transplant in pill form. The healthy pets that serve as AnimalBiome’s donors must pass a rigorous selection process, including DNA testing for microbiome composition, and an extensive pathogens and parasites screen every time we collect from our donors. Our screening process ensures that patients do not have the additional health risks due to exposure to diseases and pathogens.

AnimalBiome Veterinary is The Leader in FMT for Pets

AnimalBiome maintains the world’s largest stool bank for cats and dogs. We lead the way in best practices for FMT donor material, including rigorous screening of donor feces and screening of the donors themselves for health, medication history, behavior, and microbiome composition.18

We’ve also set the benchmark for how to conduct pet microbiome studies and helped pet food companies determine whether their products are microbiome-friendly.18

Information on the Material Used in Our Fecal Transplant Capsules

Our Gut Restore Supplements for cats and dogs are derived from stool donated by healthy household pets that meet the following criteria:

  • no current or prior health issues
  • no antibiotic treatment in the prior six months
  • diverse, species-rich microbiomes (based on DNA sequencing)
  • good fecal consistency
  • healthy body weight
  • good temperament


Donor stool samples are submitted for parasites and pathogen screening to the Idexx Reference Laboratories, a leading veterinary diagnostics company, which has stringent quality control guidelines and well-validated standard operating procedures.

All cat donor material is regularly screened for parasites and pathogens:

  • Cats are screened for the following pathogens via PCR: Clostridium perfringens Enterotoxin Gene, Feline coronavirus, Tritrichomonas foetus, Campylobacter coli, Campylobacter jejuni, Feline panleukopenia virus, Clostridium perfringens Alpha Toxin, Cryptosporidium, Salmonella spp, Toxoplasma gondii, Giardia
  • Cats are screened for the following parasites via ELISA: Giardia, Hookworms, Whipworms, Roundworms
  • Cats are screened for ova and parasites using fecal flotation.


All dog donor material is regularly screened for parasites and pathogens:

  • Dogs are screened for the following pathogens via PCR: Clostridium perfringens CPnetEF toxin gene, Clostridium perfringens Enterotoxin Gene, Campylobacter coli, Campylobacter jejuni, canine distemper virus, canine enteric coronavirus, canine parvovirus 2, canine circovirus, Clostridium difficile toxin A, Clostridium difficile toxin B, Cryptosporidium spp., Giardia spp., Salmonella spp.
  • Dogs are screened for the following parasites via ELISA: Hookworms, Roundworms, and Whipworms
  • Dogs are screened for ova and parasites using fecal flotation.


  1. Marsilio S, Pilla R, Sarawichitr B, Chow B, Hill SL, Ackermann MR, et al. Characterization of the fecal microbiome in cats with inflammatory bowel disease or alimentary small cell lymphoma. Sci Rep. 2019;9(1):19208. doi.org/10.1038/s41598-019-55691-w 
  2. Craig JM. Atopic dermatitis and the intestinal microbiota in humans and dogs. Vet Med Sci. 2016;2(2):95-105. doi.org/10.1002/vms3.24 
  3. Kerem U. Fecal microbiota transplantation capsule therapy via oral route for combatting atopic dermatitis in dogs. Ankara Üniversitesi Veteriner Fakültesi Dergisi. 2022;69(2):211-219. doi.org/10.33988/auvfd.822971 
  4. Shi N, Li N, Duan X, Niu H. Interaction between the gut microbiome and mucosal immune system. Mil Med Res. 2017;4:14. doi.org/10.1186/s40779-017-0122-9 
  5. Niina A, Kibe R, Suzuki R, Yuchi Y, Teshima T, Matsumoto H, et al. Improvement in Clinical Symptoms and Fecal Microbiome After Fecal Microbiota Transplantation in a Dog with Inflammatory Bowel Disease. Vet Med (Auckl). 2019;10:197-201. doi.org/10.2147/VMRR.S230862 
  6. van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013;368(5):407-415. doi.org/10.1056/NEJMoa1205037 
  7. McIlroy J, Ianiro G, Mukhopadhya I, Hansen R, Hold GL. Review article: the gut microbiome in inflammatory bowel disease-avenues for microbial management. Aliment Pharmacol Ther. 2018;47(1):26-42. doi.org/10.1111/apt.14384 
  8. Schepici G, Silvestro S, Bramanti P, Mazzon E. The Gut Microbiota in Multiple Sclerosis: An Overview of Clinical Trials. Cell Transplant. 2019;28(12):1507-1527. doi.org/10.1177/0963689719873890 
  9. Żebrowska P, Łaczmańska I, Łaczmański Ł. Future Directions in Reducing Gastrointestinal Disorders in Children With ASD Using Fecal Microbiota Transplantation. Front Cell Infect Microbiol. 2021;11:630052. doi.org/10.3389/fcimb.2021.630052 
  10. de Groot P, Nikolic T, Pellegrini S, Sordi V, Imangaliyev S, Rampanelli E, et al. Faecal microbiota transplantation halts progression of human new-onset type 1 diabetes in a randomised controlled trial. Gut. 2021;70(1):92-105. doi.org/10.1136/gutjnl-2020-322630 
  11. Mullen KR, Yasuda K, Divers TJ, Weese JS. Equine faecal microbiota transplant: Current knowledge, proposed guidelines and future directions. Equine Vet Educ. 2018;30(3):151-160. doi.org/10.1111/eve.12559 
  12. DePeters, E. J., and L. W. George. "Rumen transfaunation." Immunology letters 162, no. 2 (2014): 69-76. doi.org/10.1016/j.imlet.2014.05.009 
  13. Pereira GQ, Gomes LA, Santos IS, Alfieri AF, Weese JS, Costa MC. Fecal microbiota transplantation in puppies with canine parvovirus infection. J Vet Intern Med. 2018;32(2):707-711. doi.org/10.1111/jvim.15072 
  14. Tuniyazi M, Hu X, Fu Y, Zhang N. Canine Fecal Microbiota Transplantation: Current Application and Possible Mechanisms. Vet Sci China. 2022;9(8). doi:10.3390/vetsci9080396
  15. Penders J, Stobberingh EE, van den Brandt PA, Thijs C. The role of the intestinal microbiota in the development of atopic disorders. Allergy. 2007;62(11):1223-1236. doi.org/10.1111/j.1398-9995.2007.01462.x 
  16. Nuttall TJ, Marsella R, Rosenbaum MR, Gonzales AJ, Fadok VA. Update on pathogenesis, diagnosis, and treatment of atopic dermatitis in dogs. J Am Vet Med Assoc. 2019;254(11):1291-1300. doi.org/10.2460/javma.254.11.1291 
  17. Petersen EBM, Skov L, Thyssen JP, Jensen P. Role of the Gut Microbiota in Atopic Dermatitis: A Systematic Review. Acta Derm Venereol. 2019;99(1):5-11. doi.org/10.2340/00015555-3008 
  18. Jarett JK, Kingsbury DD, Dahlhausen KE, Ganz HH. Best Practices for Microbiome Study Design in Companion Animal Research. Front Vet Sci. 2021;8:644836. doi.org/10.3389/fvets.2021.644836