Fecal Microbiota Transplant (FMT)

Fecal transplant? It might sound strange or gross, but fecal microbiota transplant (FMT) is actually a well-established treatment approach that has been used effectively in both humans and animals for a long time. So what exactly is FMT? And what makes it such a promising solution for many conditions and diseases in people and pets?

What Is a Fecal Microbiota Transplant (FMT)?

A fecal microbiota transplant (FMT), also called a fecal transplant, is the transfer of stool from a healthy donor to the gastrointestinal (GI) tract of a sick recipient. That transfer can be done in clinic (via colonoscopy, enema, or endoscopy) or with oral capsules. The stool from the donor contains a diverse, well-functioning community of bacteria that take up residence in the recipient’s gut.

By providing a complete set of healthy, species-appropriate gut microbes, FMT can resolve a variety of symptoms associated with imbalance or dysfunction of the gut microbiome—including digestive disorders like inflammatory bowel disease (IBD), skin problems like atopic dermatitis, and various immune system issues. FMT even has the potential to correct obesity: several studies in mice have found that transplanting fecal material from lean mice into the intestines of obese mice transfers metabolic benefits, allowing the recipient mice to achieve a healthier weight.

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

How Long Has FMT Been Used in Humans?

FMT has been used in human medicine for thousands of years. The transfer of fecal material from a healthy person to a sick 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.)

Though modern regulatory entities like the Food and Drug Administration (FDA) are still determining how to classify it, FMT continues to demonstrate beneficial results for a growing list of human health conditions.

For example, FMT is routinely used in human medicine to treat 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). 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. A recent study demonstrated that FMT can be used to stop the progression of type 1 diabetes in humans.

What about FMT in Animals?

FMT has been used in large-animal veterinary medicine since the 17th century. (In cattle and horses, the practice is often called “transfaunation.”) 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.

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

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 Is FMT Administered?

In both humans and animals, FMT can be delivered in clinic (via colonoscopy, enema, or endoscopy) or with oral capsules. For cats and dogs, colonoscopies, enemas, and endoscopies can be expensive and generally require sedation. That’s why AnimalBiome 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 Gut Restore Supplement is an oral FMT capsule that gives your pet the benefits of FMT without the need for surgery or sedation. Our Gut Restore capsules (aka “poop pills”) deliver viable bacterial cells in a proprietary mixture of carefully screened, cryoprotected, freeze-dried donor stool. Stable at room temperature, the capsules offer a noninvasive, affordable, at-home alternative for pets suffering from digestive, skin, or immune system issues.

What Symptoms or Conditions Can FMT 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 problems, we’re sure to learn about more conditions that can be helped by FMT.

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 issues and skin issues.

Digestive Issues

Digestive symptoms such as diarrhea, constipation, vomiting, and weight loss can have many different causes. If you and your veterinarian have already worked together to rule out other explanations (such as food sensitivities, parasites, and underlying disease), the next thing to check is whether your pet has an imbalanced gut microbiome.  

For example, the genus Escherichia (a group of bacteria that includes E. coli) 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 uncomfortable digestive issues.

FMT can resolve diarrhea quickly by introducing a whole community of beneficial bacteria that crowd out the harmful ones, restoring healthy function to the digestive system.

Read more about common causes of diarrhea and at-home remedies:

Skin Issues

Research has shown that long-lasting or recurring skin issues—such as red or itchy skin, hair loss, chin acne, and recurrent ear infections—have a connection to the gut microbiome. That’s because skin conditions are often caused by a defective immune system response, and most of the body’s immune cells live in the GI tract.

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’s associated with food allergies). Both of these effects—a compromised immune system and a leaky gut—can show up as skin problems. A dysfunctional gut environment is also more prone to inflammation, which can trigger hyperactive immune responses all over the body.

Itching and other skin problems may be a clue that your pet’s gut microbiome is missing some key bacteria groups.

How Does FMT Work?

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

When pets with digestive symptoms, skin issues, or immune system problems turn out to be missing certain important gut bacteria, we need to add those missing members to the microbiome and help the new populations grow and thrive.

The Gut Restore Supplement provides a whole community of healthy cat- or dog-specific microbes. The capsule’s enteric coating prevents it from dissolving until it reaches the intestines, where the contents seed your pet’s gut with a diverse array of healthy bacteria, restoring any missing groups.

If instead of identifying missing beneficial groups, your pet’s Gut Health Test report shows an overgrowth of harmful bacteria, restoring balance will require removing or reducing those troublemaking groups. FMT capsules can help in this scenario too, removing harmful bacteria through a process called “competitive exclusion.”

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

Is FMT Safe for My Pet?

Our Gut Restore Supplements are an effective, noninvasive approach that provides the benefits of a fecal transplant in pill form, without the need for surgery or sedation. The healthy pets that serve as AnimalBiome’s donors must pass a rigorous selection process, including DNA testing for microbiome composition, and all donor material is extensively screened for pathogens and parasites.

Though fecal transplants delivered via colonoscopy, enema, or endoscopy have been shown to help with multiple health conditions, in both humans and pets, there are some risks with these methods.

If the donor stool is not properly screened, there’s a chance that pathogens and/or parasites could be passed on to your cat or dog. If you choose to have a fecal transplant procedure performed by a veterinarian, it’s important to ask about their screening process for the donated fecal material.

In addition, more invasive FMT procedures generally require sedation, which has its own risks and complications.

What Makes AnimalBiome a Leader in FMT for Pets?

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

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.

Where Do You Get the Material for Your Fecal Transplant Capsules?

Our Gut Restore Supplements for cats and dogs are derived from stool donated by healthy pets that live in homes and 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.