Microbiome restorative therapy in companion animals

A procedure in which fecal material is transferred from a healthy individual to the gastrointestinal tract of an ailing individual, MBRT helps balance the microbiome and treat digestive issues.

The microbiome is a characteristic community of microorganisms (bacteria, fungi, viruses and other microbes) occupying a well-defined habitat, such as in or on an animal’s body.1 Mammals are exposed to their first microbes during birth and through breastfeeding.2 These early life events contribute to each animal having a unique gut microbiome signature. The microbes that are first to arrive in a particular habitat can affect which new species will be able to colonize later on. In other words, these early life events are foundational and will influence a cat or dog’s health for the rest of his life. Research on the gut microbiome suggests it plays essential roles in host digestion, immunity, the central nervous system, behavior (including anxiety and depression), skin health, obesity and other metabolic disorders.3

The missing microbes

A young animal may fail to get the full complement of beneficial microbes if the mother is missing them herself, or if the young animal is orphaned or weaned too early. Even if a healthy microbiome is established early in life, microbes in the gut will change with age, diet and lifestyle. The gut microbiome may also be depleted or harmed by exposure to broad spectrum antibiotics that kill both harmful and beneficial microbes. The widespread use of antibiotics and antimicrobials may be contributing to increased incidences of conditions such as inflammatory bowel disease (including Crohn’s disease and ulcerative colitis), esophageal reflux, Type 1 diabetes, asthma, and food allergies in human populations.4 Food additives and non-steroidal anti-inflammatory drugs (NSAIDs) have also been shown to alter the composition of the gut microbiome,5 and may further contribute to the development of chronic digestive conditions in companion animals. The widespread use of antibiotics and other medications may also contribute to why digestive issues are a top reason for veterinary visits in both cats and dogs.

Do feral cats have healthier microbiomes?

In a citizen science project called KittyBiome,6 microbiome samples were collected from domestic cats living in shelters, households (both indoor and outdoor cats), and outside (feral). Samples from wild cats, including black-footed cats, cheetahs, lions and leopards, were also collected. Many house cats had depleted microbiomes with low bacterial diversity when compared to adult feral cats and their wild cousins, and 20% suffered from a chronic digestive condition.

The research showed that diet played a large role in the composition and diversity of gut bacteria. Cats fed a raw diet tended to have greater bacterial diversity and increased representation of bacteria associated with the production of the short chain fatty acid, butyrate (AnimalBiome unpublished data).7 Butyrate is produced by bacterial fermentation of dietary fiber and is a critical mediator of the inflammatory response in the gut microbiome.

Participants in the study wanted to know how to restore their cats’ health. Many had already tried using antibiotics, steroids and dietary modifications, including prescription diets, and were looking for other solutions.

MBRT can replace missing microbes

One approach to rebuilding the gut microbiome is Microbiome Restorative Therapy (MBRT), a procedure in which fecal material is transferred from a healthy individual to the gastrointestinal tract of an ailing individual. Although its use in human medicine has only begun to increase in recent years, MBRT (also known as transfaunation or fecal microbiota transplantation [FMT]) has been used in veterinary practice since at least the 18th century for cattle, horses, sheep and other animals suffering from rumination disorders, indigestion and colitis.8,9,10

Interest in the application of MBRT in small animal practice is growing, particularly for digestive disorders. Despite pioneering integrative veterinarians like Dr.Margo Roman (mashvet.com), who has performed >2,000 MBRT procedures in the past ten years, MBRT is still not widely used at this point in conventional practice11 (see Dr. Roman’s article on MBRT in IVC Journal, Volume 4, Issue 4, or at ivcjournal.com/mbrt-immune-system). In contrast, there has been tremendous interest in the application of FMTs in human medicine, particularly in the treatment of Clostridium difficile infections that are not responsive to antibiotics, as well as Crohn’s disease, ulcerative colitis, constipation and enterocolitis. Studies have shown that it is possible to introduce microbes from a donor into the microbiome of a recipient, where they are maintained, at least for a period of time. A growing number of integrative veterinarians offer MBRT as a way to provide microbial supplementation to patients from a healthy live donor of the same species. One factor restricting the growth of MBRT in practice is the availability of screened fecal material from healthy donors.

To create a bank of carefully-screened fecal material from healthy donors, a variety of factors must be considered. In addition to standard pathogen and parasite screening, donors must have no current or past health concerns, whether physical or behavioral; and they must have no history of systemic antibiotic use. These “golden-poo pets” must also be old enough to have developed a sufficiently diverse microbiome, but young enough for that diversity to still be intact.

Fecal transplants may be administered in three ways, often depending on the severity of the ailment:

  • Rectally, via enema and colonoscopy (typically uses fresh or frozen material). This method may be needed in more critical cases.
  • Orally, via nasoduodenal intubation and enteroscopy (typically uses fresh or frozen material).
  • Orally, via enteric-coated capsules sold only to veterinarians. The capsules contain pre-screened material prepared with all-natural ingredients that remain stable at room temperature while retaining high viability. Enteric coatings are made of long-chain carbohydrates that prevent capsule contents from being destroyed by stomach acid.


Scientists haven’t even begun describing many of the common organisms living in the microbiomes of healthy dogs and cats. For example, recent research identified more than 20 bacterial strains that are new to science, in a single sample of cat poop. This makes it difficult to develop a supplement that contains the full spectrum of genera found in healthy dogs and cats. Probiotic strains that are not cat- or dog-specific may be helpful for controlling clinical signs of disease, but will not typically colonize the host. This means they must be given continuously in order to see an effect.

MBRT provides a “complete package” because it reflects the abundance of bacteria, fungi and bacteriophages in the relative ratios found in a healthy cat or dog.

Top ten uses for MBRT

  1. Chronic diarrhea
  2. Chronic vomiting
  3. Recovery from antibiotic treatment
  4. Constipation
  5. Inappetence and poor body condition
  6. Food sensitivities
  7. Hemorrhagic gastroenteritis
  8. Skin conditions, including atopic dermatitis
  9. Decreased gut motility and difficulty passing hairballs
  10.  Fecal incontinence

For more information visit AnimalBiome.com, mashvet.com, and read Dr. Roman’s article on MBRT.

Case report – an application of MBRT for IBD

Laila, an active boxer mix, was the picture of health until she turned five. Over the course of just a few months, she developed severe diarrhea and vomiting. She was given antibiotics, antacids, probiotics and prescription diets, but nothing seemed to alleviate her symptoms and she continued to worsen.

After an official IBD diagnosis, she began a high daily dose of prednisone in addition to her other medications. Her diarrhea temporarily resolved, but after lowering the prednisone dosage to minimize side effects, Laila relapsed. She once again developed watery diarrhea, and it was not alleviated even after significantly increasing the prednisone dosage. Instead of resolving her digestive issues, in fact, the prednisone increase prompted an onset of medication-induced Cushing’s disease, turning this once energetic muscular dog into a frail low-energy one. Despite the steroid, her digestive issues persisted.

Finally, Laila was tried on oral Gut Restoration capsules for MBRT. Slowly, the consistency of her feces changed from a yellowish liquid to a healthy brown solid, and she has since been tapered off all prescription medications. Most importantly, her health and happiness have improved beyond measure.

The chart shows Laila’s gut microbiome prior to taking the capsules, compared with that of a healthy dog. Her sample indicated an absence of bacteria commonly found in dogs, including Prevotella, Fusobacterium, Bacteroides and Megamonas, which are found in 84%, 95%, 97% and 93% of healthy dogs, respectively.


1Whipps JM, Lewis K, Cooke, RC. 1988. “Mycoparasitism and plant disease control” 161-87.in NM Burge Editor, Fungi in Biological Control Systems. Manchester University Press.

2Pannaraj PS, Li F, Cerini C, Bender JM, Yang S, Rollie A, Adisetiyo H, Zabih S, Lincez PJ, Bittinger K, Bailey A. 2017. “Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome”. JAMA pediatrics.

3Yong E. 2016. I Contain Multitudes: The microbes within us and a grander view of life. Random House.

4Blaser MJ. 2014. Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues, Macmillan.

5Igarashi H, Maeda S, Ohno K, Horigome A, Odamaki T, Tsujimoto, H. 2014. “Effect of oral administration of metronidazole or prednisolone on fecal microbiota in dogs”. PloS one, 9(9), p.e107909.

6Dahlhausen K, Krebs BL, Watters JV, Ganz, HH. 2016. “Crowdfunding campaigns help researchers launch projects and generate outreach”. Journal of microbiology & biology education, 17(1), p.32.

7AnimalBiome – unpublished data –CHRISTINA TO PROVIDE REST OF REFERNCE

8Brag S, Hansen HJ. 1994. “Treatment of ruminal indigestion according to popular belief in Sweden”. Revue scientifique et technique (International Office of Epizootics), 13(2), pp.529-535.

9Rager KD, George LW, House JK, DePeters EJ. 2004. “Evaluation of rumen transfaunation after surgical correction of left-sided displacement of the abomasum in cows”. Journal of the American Veterinary Medical Association, 225(6), pp.915-920.

10DePeters EJ, George LW. 2014. “Rumen transfaunation”. Immunology Letters, 162(2), pp.69-76.

11Chaitman J, Jergens AE, Gaschen F, Garcia-Mazcorro JF, Marks SL, Marroquin-Cardona AG, Richter K, Rossi G, Suchodolski JS, Weese JS. 2016. “Commentary on key aspects of fecal microbiota transplantation in small animal practice”. Veterinary Medicine: Research & Reports, 7, pp.71-74.