Fecal Transplants for Dogs

Fecal transplants can help dogs with chronic digestive problems recover their health, by helping them build an improved microbiome.


The term alone is a conversation-stopper. Fecal transplants? For dogs? Don’t laugh. Fecal transplants are making headlines as a wonder drug for pets and people.

Forty years ago, when Clostridium difficile colitis, or “C. diff,” a bacterial infection resulting from antibiotic therapy, became an epidemic in American hospitals, nothing cured its debilitating, non-stop diarrhea. For most patients, as soon as an effective treatment was discontinued, symptoms returned. Finally, doctors tried a technique that had been successfully used decades earlier but which wasn’t formally adopted because the thought of it made people uncomfortable. When fecal matter from healthy donors was transferred to the colons of sick patients, more than 90 percent recovered. Their symptoms resolved within hours and never returned.

Veterinarians who gave fecal transplants to puppies with chronic diarrhea, or to adult dogs with gastrointestinal problems, reported similar success rates.

dog looking uncertain

Transferring microbial material from healthy to sick ruminants, such as cattle, is a long-established veterinary practice, but fecal microbial transplantation, or FMT, is so new to veterinary medicine that much remains unknown. As a result, the treatment is controversial and not widely available, though a growing number of veterinarians and caregivers are exploring this option. Understanding your dog’s microbiota and the history of fecal transplants will help you make informed decisions for your best friend regarding the treatment and prevention of gastrointestinal illnesses.

A Dog’s Microbiome

The term “microbiome” was coined by molecular biologist Joshua Lederberg, recipient of the 1958 Nobel Prize in Medicine, to signify the ecological community of commensal (living cooperatively on or within another organism), symbiotic (living in close and mutually beneficial proximity), and pathogenic (capable of causing disease) microorganisms that share the body’s space.

Today “microbiome” is an umbrella term used to describe communities of bacteria, viruses, fungi, and other microbes in the body. Most intestinal microbes reside in the cecum, which is a “pocket” of the large intestine, where they are known as the “gut microbiome.”

Bacteria are the most studied of these microorganisms, and the terms “microbiota” and “microflora” describe bacterial communities on mucosal and skin surfaces. The human body contains more than a thousand separate species of bacteria, most of which are important to health and some of which can cause disease.

Little attention was paid to the microbiome until testing methods, such as whole genome sequencing, made the National Institutes of Health’s Human Microbiome Project (HMP) and related research possible. The HMP, a five-year study launched in 2008, explored connections between changes in the microbiome and human health and disease.

Dogs have microbiomes, too. In fact, studies have found that people and dogs living in the same household share much of the same microbiome. Complex colonies of microorganisms live in the ears, mouth, respiratory tract, and skin, but most occupy the digestive tract.

What is a Gut Microbiome?

A healthy microbiome destroys harmful pathogens, including disease-causing viruses, fungi, bacteria, and parasites. As a result, the microbiome is the immune system’s first line of defense. Differences in microbiomes help explain why some dogs exposed to diseases like parvovirus, distemper, leptospirosis, Lyme disease, canine flu, heartworm, or kennel cough get sick while others remain symptom-free.

“Friendly” or beneficial bacteria secrete chemicals that destroy harmful bacteria and, if they are present in sufficient numbers, colonies of beneficial bacteria starve harmful microbes by depriving them of nutrients and space.

In addition, the microbes in a healthy microbiome can bind to toxins, such as allergens and substances that cause cancer, removing them from the body through normal elimination.

The mucus membrane that lines the gastrointestinal tract from esophagus to colon contains lymphocytes and macrophages, which are different types of white blood cells that attack or disable agents of infection. This membrane, the gut-associated lymphoid tissue (GALT), prevents digestion-improving bacteria from penetrating other tissues or entering the bloodstream, where they can cause damage.

A healthy microbiome not only improves a dog’s digestion, but also creates some nutrients, including thiamin (vitamin B1), cobalamin (vitamin B12), and short-chain fatty acids that help your dog absorb minerals such as calcium, iron, and magnesium.

In addition, the microbiome helps regulate the body’s endocrine system and metabolism, and there are links between the microbiome and mental health. In short, the microbiome affects nearly every aspect of your dog’s health and happiness.

Microbiome Diversity in Dogs

Yuki is a McNab Shepherd-mix, currently 15.5 years old, owned by Holly Ganz, PhD, AnimalBiome’s co-founder and CEO. About two years ago, Yuki began exhibiting clinical signs of hemorrhagic gastroenteritis (HGE) nearly once a month. She was able to eat only a chicken and rice-based kibble and one treat that contained only chicken. Other foods would trigger bouts of bloody diarrhea and it would take a couple of weeks for her stools to become normal.

Starting in late April 2017, Yuki was given AnimalBiome’s Gut Restoration System for dogs. The capsules were given twice a day for four weeks.

While taking the capsules, Yuki’s stools improved in consistency and color and continued to improve in the following month. Subsequently, Ganz was able to reintroduce other protein sources and healthy treats into Yuki’s diet. She hasn’t had another bout of gastroenteritis since, and her stools continue to have a healthy consistency and color.

Below are some of the results of Yuki’s microbial analyses. The complete report shows how Yuki’s microbiome changed after receiving fecal transplants, and compares the analyses from Yuki’s fecal samples taken before and after treatment with average values of samples taken from healthy dogs. Each bacterial type found in the samples is described and its presence in the dog’s microbiome is discussed. The “ideal” microbiome is not yet identifiable, but these surveys are fascinating.

Fecal Microbiota Transplantation

The necessary ingredients for a successful fecal transplant are a healthy donor and a method for transferring material from donor to patient.

In humans, donors have often been family members or close friends. In the past few years donor banks have been created to store fecal matter from volunteers. These volunteers must be healthy, with no recent antibiotic use and no bowel disease, and who are tested for conditions including bloodborne pathogens and parasitic infections.

Human clinics mix donor feces with sterile saline solution, then homogenize and/or filter the mixture to remove particles that might clog equipment. Both fresh and frozen material has been shown to be effective. The donor’s stool can be administered orally through a nasogastric tube or rectally through a retention enema via endoscope during a colonoscopy. The latter method is often preferred because it administers the fecal suspension directly into the ileum (the small intestine’s final and longest section) and the entire colon.

There are not yet any commonly accepted guidelines for canine donors, though of course health is an obvious concern. Some clinics that offer FMT treatment require donor dogs, which can be any breed or size, to have a normal body weight; be free from malignancies, parasites, allergies, and gastrointestinal disease; and to not have received antibiotics within the past three months or longer. Some clinics require donor dogs to be vaccinated against specific illnesses, while others prefer no vaccinations.

In a University of Helsinki study of dogs with inflammatory bowel disease described by Jean Dodds, DVM, in an April 2017 “Fecal Microbiota Transplantation” report at her Pet Health Resource Blog, potential donor dogs were required to be naturally born (like humans, infant dogs are born sterile and acquire their first microbiota in the birth canal) and breast-fed (the mother’s colostrum and milk are important foods for the developing microbiome) and have no history of systemic antibiotic use throughout their lives, in addition to other health screenings.

Dr. Dodds recommends that if a patient needing a fecal transplant has specific food intolerances, the donor animal must eat a diet compatible to that patient for 10 to 14 days before fecal samples are obtained so that its feces do not contain reactive allergenic food residues that could harm the patient.

She also recommends that the patient not receive any antibiotics, colostrum supplements, prebiotics, probiotics, digestive enzymes, herbal bowel preparations, or heartworm, flea, or tick treatments for 10 days before the transplant.

FMT treatment sounds like a miracle cure, but it doesn’t work for every patient. In some cases, the effects of FMT have been temporary, or the procedure had to be repeated because the introduced fecal material was not effectively absorbed, or the transplanted bacteria were overwhelmed by existing medical conditions.

The cost of FMT varies according to the methods used, testing procedures, sedation, veterinary consultation, and donor screening, ranges from $500 to $1,500 or more.

The History of Fecal Transplants

For millennia, Chinese physicians used what they called “yellow soup,” made with fecal matter from healthy donors, to treat patients with food poisoning or severe diarrhea. During World War II in North Africa, Bedouin camel herders gave the stool of healthy camels (a traditional treatment for diarrhea) to German soldiers with bacterial dysentery. Sick ruminants have long been treated for similar symptoms with the cud of healthy animals.

But it wasn’t until Ben Eiseman, MD, Chief of Surgery at Denver General Hospital, successfully treated four patients for chronic diarrhea caused by a painful colon inflammation associated with Clostridium difficile that human fecal transplants appeared in the medical literature. His report in the November 1958 journal Surgery described how retention enemas containing the stool of healthy donors cured patients within hours.

Dr. Thomas Borody, an Australian gastroenterologist, began experimenting with human fecal transplants when a patient developed incurable colitis after vacationing in Fiji in the 1980s. Searching the medical literature for alternative treatments, he found Dr. Eiseman’s paper and, using stool donated by the patient’s brother, administered the material by enema on two consecutive days. The patient’s diarrhea quickly disappeared and never returned.

In 2014, ABC News interviewed Dr. Borody about his 25 years of experience with fecal microbiota transplantation (FMT). He claimed that in addition to quickly clearing C. diff infections, FMT has successfully treated other gastrointestinal problems such as colitis and Crohn’s disease – and, more controversially – he considers the gut a gateway for toxins to enter the body, triggering diseases like rheumatoid arthritis, Parkinson’s, and autism.

The U.S. Food and Drug Administration approves FMT for only one condition: recurrent C. difficile infections. There are as yet no official guidelines for the veterinary applications of FMT.

Dysbiosis and Inflammatory Bowel Disease (IBD) in Dogs

The term “dysbiosis” describes weakened or depleted beneficial microbes such as those that make up the microbiome. As soon as the body’s population of beneficial microbes declines, pathogens begin to crowd them out, resulting in nutritional deficiencies and illnesses, including inflammatory bowel disease, or IBD. The main symptoms of inflammatory bowel disease in dogs are vomiting, diarrhea, and weight loss with, in some cases, blood or mucus in the stool.

What causes dysbiosis? While most of the blame goes to antibiotics – the wonder drugs that destroy beneficial as well as harmful bacteria – researchers list additional contributing causes such as processed foods, genetically modified foods, pesticides, chemical preservatives, pasteurization and other enzyme-destroying treatments that kill germs in food, vaccines, prescription drugs, and the stresses of modern life.

Dysbiosis contributes to leaky gut syndrome, in which undigested or partially digested food particles move through the digestive tract’s mucous lining and enter the blood stream. This can happen when the mucous lining shrinks and thins, leading to injury and inflammation. Leaky gut syndrome has been blamed for a variety of symptoms and illnesses, including food allergies, hot spots, skin irritations, yeast infections, diarrhea, constipation, inflammatory bowel disease, autoimmune disorders, joint pain, imbalances involving the liver or pancreas, thyroid problems, weight gain, diabetes, slow metabolism, and low energy.

The methods most frequently suggested for reversing dysbiosis include avoiding antibiotics, pesticides, prescription drugs, and toxins, all of which – especially antibiotics – can damage the microbiome. Feeding fresh, whole foods rather than sterilized processed foods is recommended because fresh foods contain bacteria that support the microbiome. Daily outdoor exercise supports the microbiome by exposing a dog to many naturally occurring microbes. Probiotic supplements are often recommended, although there is disagreement as to which products work well for dogs and which best survive a dog’s high concentrations of stomach acid. Other probiotic sources include foods that are themselves rich in beneficial bacteria, such as naturally fermented vegetables. Foods and supplements containing prebiotics, or fiber that nourishes beneficial bacteria, support the microbiome as well.

As effective as probiotics can be in preventive medicine, when a dog has inflammatory bowel disease, probiotics are unlikely to help. In fact, there is no scientific support for their therapeutic use in canine IBD.

Human IBD is difficult to diagnose and usually involves intestinal biopsies, but identifying IBD in dogs should become easier thanks to a unique pattern of microbes that accompanies the illness. In October 2016, the journal Nature Microbiologyreported that researchers at the University of California San Diego School of Medicine analyzed fecal samples from dogs with and without IBD and discovered that they were able to predict which dogs had the disease with more than 90 percent accuracy. While there is not yet a veterinary test for canine IBD, diagnosing the illness with a simple stool sample may be possible in the future.

Can Poop Treat Other Medical Issues?

While there are no clinical trials proving any of the following claims, veterinarians who use FMT believe that it does far more than repair a dog’s digestion.

For example, Dr. Margo Roman says that when a dog’s unbalanced microbiome becomes healthy, symptoms like behavioral problems, aggression, skin and coat problems, and even coprophagia (stool eating) disappear. She has used FMT in the treatment of canine liver failure, kidney failure, allergies, adrenal exhaustion, atypical Addison’s disease, atypical Cushing’s disease, and methicillin-resistant Staphylococcus aureus (MRSA).

Dr. Thomas Borody considers FMT a possible treatment for humans with Parkinson’s disease, autism, and rheumatoid arthritis, and other physicians claim it may help prevent or treat Alzheimer’s disease, depression, acne, type 2 diabetes, cancer, and more.

In many cases such theories are based on observations that may be coincidental, such as when a patient with rheumatoid arthritis is treated with FMT for a digestive disorder and the arthritis symptoms diminish along with the patient’s diarrhea.

In these early days of FMT therapy, it’s impossible to know how the treatment really works or what benefits it may offer. After all, Western medicine is just beginning to look at fecal matter as something other than waste. But with the microbiome becoming a hot medical research topic, we can expect to learn much more in the years ahead.

Poop Pills for Dogs

With their need for special equipment and sedation, Microbial Fecal Transplantation procedures can be expensive and time-consuming. Wouldn’t it be simpler just to give a dog some pills to swallow?

Yes, says microbial ecologist Holly Ganz, PhD, co-founder and CEO of AnimalBiome, a company that analyzes the microbiomes of dogs and cats and offers treatment in the form of healthy fecal material in capsules. “Our microbiome assessment kits can help you and your veterinarian determine whether your pet’s disorder is linked to an imbalanced gut microbiome,” she explains.

The $95 analysis identifies all of the bacteria in a dog’s fecal sample, establishes a baseline profile of the dog’s gut health, and compares it to the microbiome profiles of other dogs. Learning whether a dog’s digestive disorder is linked to a bacterial imbalance, or discovering an imbalance before it affects the animal’s health, can help veterinarians and caregivers make appropriate changes in diet, lifestyle, or medical treatment.

For dogs with symptoms of inflammatory bowel disease or similar disorders, AnimalBiome offers capsules containing fecal matter from donor dogs who are screened for health, age, fecal consistency, behavior, and microbiome composition based on Illumina sequencing of amplified 16S rRNA. Donated material is quarantined for at least 30 days to ensure that the donors remained healthy. Donors regularly go outdoors for walks, have not had antibiotic treatment in the prior six months, have diverse microbiomes, and are not overweight.

Pathogen screening for donor dogs includes Clostridium perfringens antigen, Clostridium perfringens alpha toxin, Clostridium perfringens beta toxin, Clostridium difficile toxin A, Clostridium difficile toxin B, Cryptosporidium spp, Salmonella spp, Giardia spp, and Canine Parvovirus 2.

AnimalBiome charges $200 for the capsules; but for $300 you can get the capsules plus before and after microbiome assessments.

Do capsules work? Though no one has conducted clinical trials with dogs, the human research is encouraging.

In a 2014 study conducted by researchers from Massachusetts General Hospital, Boston Children’s Hospital, Harvard Medical School, and Tel Aviv University, 20 patients ranging in age from 11 to 89 who had at least three episodes of recurrent C. difficile infection took 15 stool capsules from pre-screened, healthy donors over a two-day period. In 14 of the patients, diarrhea resolved after the first treatment. The remaining six patients were treated again, and four of them recovered. None of the successfully treated patients experienced a recurrence of symptoms in the following eight weeks, resulting in a 90 percent success rate.

Invasive means do not need to be used to deliver the transplant. “The study showed you can use frozen donor stool successfully and safely,” says the study’s co-author, pediatric gastroenterologist George H. Russell, MD, MS.

But My Dog Already Eats Poop!

Early proponents of so-called “evolutionary” or “biologically appropriate raw diets” have noted that the droppings of healthy herbivores, including deer, elk, sheep, and cattle, are a treasure trove of probiotics, prebiotics, and other nutrients. In her Complete Herbal Handbook for the Dog and Cat (Farrar, Straus and Giroux, 1991), Juliette de Bairacli Levy wrote, “Dogs should never have their natural instincts thwarted in the matter of diet. They should not be prevented from eating the droppings of grass-fed cattle and horses, from which they can get many vital elements derived from the herbage on which the animals have grazed and in a form easily assimilated by the dog.”

In his popular book, Give Your Dog a Bone: The Practical Commonsense Way to Feed Dogs for a Long Healthy Life (Warrigal Publishing, 1993), Australian veterinarian Ian Billinghurst reminded readers that all dogs are scavengers. “They receive valuable nutrients from material we humans find totally repugnant,” he said, “things like vomit, feces, and decaying flesh… Feces are a highly valuable food consisting of the dead and living bodies of millions upon millions of bacteria.”

The manure of deer, elk, cattle, sheep, geese, and other grass-eating animals contains B-complex vitamins, vitamin K, minerals, beneficial bacteria, essential fatty acids, enzymes, antioxidants, and fiber.

The obvious problem with free-range poop-eating is that the donors of ingested fecal matter might be ill, have an imbalanced or damaged microbiome, carry a contagious disease, or contain parasites such as Giardia, Coccidia, roundworms, tapeworms, or whipworms. Livestock droppings may also contain medications such as ivermectin used for deworming that could make your dog sick.

For farm dogs and dogs in rural areas, the benefits of eating manure probably outweigh the risks, but coprophagia (a dog’s habit of eating its own stool or that of other dogs) can cause problems. Eating his own stool won’t expose a dog to new microorganisms that could bring balance to his microbiome – and consumption of the droppings of dogs with an unknown health status is inadvisable.

However, consuming the stool of a healthy dog with a vigorous microbiome may be just what the doctor ordered – and in this case the doctor is holistic veterinarian Margo Roman, DVM, at the Main Street Animal Services of Hopkinton (MASH Clinic). Her first stool-treatment patient was Stovin, a Standard Poodle who was diagnosed with inflammatory bowel disease as a nine-week-old puppy. When he arrived at MASH in 2012, he was three years old, weighed 43 pounds, was unable to walk, and was taking a cocktail of antibiotics. His owner had already spent $16,000 on testing, medications, and blood transfusions, to no avail.

Stovin’s initial treatment, which included acupuncture and the replacement of prescription medications with nutritional supplements, resolved his intestinal distress and his health improved. Then, in an effort to reverse the effects of prolonged antibiotic treatment, Dr. Roman had Stovin ingest stool from her own healthy, organically raised dog. She had been thinking about this approach for years, she says. “Dogs eat poop anyway. I wouldn’t be doing anything that they don’t already do – I’m just directing them toward the right poop to eat.”

Stovin’s recovery was so impressive that MASH Clinic veterinarians went on to perform more than 5,000 fecal transfers on dogs and cats to treat IBD, C. difficile, C. perfringens, Giardia, and other problems.

Dr. Roman puts patients on a fresh, raw diet of GMO-free foods supplemented by probiotics, colostrum, nutraceuticals, and glandular supplements that support gut health. She reports that when a patient is prepared in this way, the fecal transplant usually works in a single treatment.

To perform the transplant, she combines healthy fecal matter with sterile saline in a blender, then filters it to remove large pieces. She applies the blended fecal matter with a syringe into the rectum.

Some dogs need repeated transplants, in which case their owners come by Dr. Roman’s clinic, pick up a bag of poop, take it home, and keep it in the freezer. When their dog starts having an issue, she says, they pop a piece of the frozen poop down the dog’s throat, and he gets better.

For more about Microbiome Restorative Therapy and Dr. Roman’s approach to gut health, see her blog, Eat Sh*t & Live.

Stool Transplant Results

As Dr. Dodds explained in her Fecal Microbiota Transplantation report, the practice of FMT has been used in veterinary medicine for years. “Since clinical trials or pilot studies were not completed,” she wrote, “these FMT procedures are considered anecdotal. However, there is nothing wrong with anecdotes because they can encourage the medical community to conduct clinical trials that give us more concrete and definite answers as well as point us in proper directions.”

One report from the March 24, 2016 Bradenton Herald in Bradenton, Florida, describes the work of Kevin Conrad, DVM, at Southeastern Guide Dogs in Palmetto, Florida. Dr. Conrad had been looking for a better way to treat dogs with recurrent diarrhea when he discovered FMT. “We see 250 dogs a year, and there were a lot of repeat offenders with symptoms not going away,” he said. “We’d either repeat antibiotics or adjust their feeding. It could take days, weeks, or months to get one dog feeling better, and I knew there had to be an easier process.”

Dr. Conrad took stool from healthy dogs, screened it by culturing microbes to check for certain bacteria, then liquified the stool and injected it into the intestines of sick puppies with a rectal tube. Within 12 to 24 hours, their symptoms began to clear. He then used the method to treat adults and pregnant dogs.

sassy chihuahua

“What we tried is to do a fecal transplant on a pre-litter mom while she is pregnant, and she’s dropping a whole litter of puppies without diarrhea issues,” he said, “So now we are not only treating it but preventing it.”

At Angell Animal Medical Center in Boston, Massachusetts, Erika de Papp, DVM, considers FMT “an exciting avenue of potential therapy for chronic enteropathies.” She cites a study conducted at the Ontario Veterinary College at the University of Guelph in Canada in which FMT successfully treated dogs and cats for chronic diarrhea that did not respond to or was only moderately controlled by the standard therapies of diet manipulation, antibiotics, anti-inflammatories, and probiotics. Donor stool was screened for parasites, Giardia, Salmonella, Campylobacter, C. difficile, and (in the case of cats) Tritrichomonas foetus.

Patients received an enema to clear their intestines before receiving FMT and then a fecal suspension delivered via enema was retained in the colon for 45 minutes. The patients’ fecal microbiomes were evaluated before and after FMT through 16S rRNA gene product sequencing. Within 24 hours, their symptoms improved, and within 48 hours of treatment, the patients’ microbiomes resembled those of their donors rather than their own stool.

Noting that the success of FMT with human patients has helped the procedure gain general acceptance, Dr. de Papp said, “I hope we can convince our veterinary clients that this is not an entirely unpalatable treatment.”

The Future of FMT

Because no published peer-reviewed studies have examined the use of FMT in dogs or cats, a group of veterinarians at a 2015 international meeting of gastroenterologists formed a research committee to document the state of the art. Their report, “Commentary on key aspects of fecal microbiota transplantation in small animal practice” (J. Chaitman, et al, Veterinary Medicine: Research and Reports, May 31, 2016), addressed FMT mechanisms, indications, donor selection, preparation, administration, safety, and regulation.

There are few or no guidelines for performing FMT in small animals, and veterinarians tend to consider it for gastrointestinal disorders when there are no other options. In human medicine the use of FMT for disorders other than recurrent C. difficile infections is not yet supported by scientific evidence, and while FMT may improve the health of dogs with acute and chronic GI inflammation, diarrhea, and inflammatory bowel disease, many questions remain unanswered.

One of those questions is regulatory. Is FMT a drug? According to the US Food and Drug Administration, if fecal microbiota is intended for use to treat or prevent disease, it would be considered a drug. At this time, the Center of Veterinary Medicine has not developed a specific policy of enforcement regarding investigational new animal drug requirements for the use of fecal microbiota for transplantation, but the procedure’s status may change, especially if synthesized microbiota are developed and patented.

As the Veterinary Medicine report concluded, “Ongoing clinical and basic science research studies will bring the strength of science and clinical observation and enhance our understanding of how important the gut microbiota is to host health.”

Microbiome Clinical Trials

For information about ongoing, planned, or completed clinical trials involving dogs and the microbiome, search online for “clinical trials” and “canine fecal transplants” or “canine microbiome.”

You will find, for example, the University of Florida College of Veterinary Medicine is currently recruiting Golden Retrievers and Australian Shepherds for a clinical research trial to determine whether the types of bacteria in a dog’s gut could be a factor in allergic skin disease.

The University of Pennsylvania School of Veterinary Medicine is currently enrolling dogs with clinical signs of Canine Chronic Enteropathy (CCE, a common cause of diarrhea, vomiting, and weight loss) in a clinical trial to determine the composition of the gastrointestinal tract’s microbiome before, during, and after treatment.

For information about Fecal Microbial Transplantation research in general, visit the Fecal Transplant Foundation and The Power of Poop.


1. If your dog has chronic digestive problems (such as persistent diarrhea and/or severe gas), ask your veterinarian about a fecal microbial transplant treatment for your dog.

2. To get more information about your dog’s microbiome, send a fecal sample and $95 to AnimalBiome.com.

Freelance writer CJ Puotinen is the author of The Encyclopedia of Natural Pet Care, and other books.