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Equine Fecal Transfaunation: The Potential Power of Shared Poop

Updated: Nov 29, 2022

What is equine fecal transfaunation? Is it what I think it is? Why would I consider it for my horse? Is it safe and affordable? And most, importantly, does it work when my horse's gut is producing unusual amounts of diarrhea?

Imagine that you are an explorer in a newly discovered rainforest. You are searching for the hidden mysteries of biology that have potential to transform modern day veterinary medicine and cure diseases that plague the urban stall dweller. The biodiversity of the dark, wet understory is greater than you could possibly have imagined. The trek is exhilarating, because there is something to learn under every leaf and stone and rotting log. You have more tools to use in your search compared to the first explorer. However, you are handicapped. You can't SEE the mysteries around you. You can only infer them from your other senses and high tech gadgets. It's like exploring neighboring galaxies with infrared and radar, and it's always exciting. This is how I envision the current understanding of the equine microbiome.

To take the planetary rainforest analogy a step further, what would happen if we took all the insects, mammals, reptiles, plants and bacteria from the Amazon jungle and placed them collectively into another planet's jungle life. Would they all survive? Would they all interact together in the same way? Would they colonize and thrive? This is also how I think about the crude, but seemingly powerful tool, of equine fecal transfaunation- also known as equine fecal transplant, micriobial transplantation or microbiotherapy- but I definitely prefer the word TRANSFAUNATION! What I am interested in learning from such a proverbial planetary rainforest, is if the balance of biology from one planet's rainforest with all of it's flora and fauna, herbivores and carnivores, microscopic prey and apex predators, can be collectively whisked away to colonize another planet. If that other planet, of course, was your horse's gut creating copious amounts of diarrhea.

What is Equine Fecal Transfaunation & Does it Work?

I am, of course, referring to the extraction of a healthy donor horse's fecal balls and their subsequent processing and placement into the digestive tract of a dysbiotic horse. I'm going to go ahead and give you a summary of what I learned over the weeks of reading and interviewing straight away.

  1. Fecal transfaunation is being used more frequently by more veterinarians than I originally would have predicted.

  2. The process if relatively safe, affordable, and easy to perform by your local veterinarian.

  3. Using fecal transfaunation as a treatment for diarrhea seems to be surprisingly successful.

CONCLUSION: Equine fecal transfaunation is a fair and reasonable treatment consideration for horses suffering from chronic diarrhea. I will be discussing this procedure as a suggested treatment for more client's horses!

What exactly IS chronic diarrhea you might ask and why might fecal transfaunation help cure it? The first problem that we face in our understanding of the issues is simple nomenclature. The jungle of jargon used to taxonomize the equine microbiome, in its healthy and not so healthy state, is formidable. As diverse as species in a rainforest, we come across a tremendously amount of nomenclature when talking about dysbiosis of the equine gut. Syndromes such as fecal water syndrome, inflammatory bowel syndrome, chronic diarrhea syndrome, and leaky gut syndrome get easily mixed up with the "itis's" like enterocolitis and duodenitis-proximal jejunitis. It's very easy to get confused. So, allow me to clarify. Lindroth (2020) defines diarrhea as "increased defecation frequency of faeces containing higher content of water and lower content of dry matter compared with normally observed in healthy horses." What we are talking about here is EXCESSIVE, CHRONIC diarrhea that doesn't go away a week after a) new forage/feed/pasture changes, b) antibiotic administration, or c) with diseases such as Potomac Horse Fever. Fecal water syndrome is characterized more specifically. According to Lindroth (2020), the water and fecal balls are excreted separately where the free water comes before or after expulsion of the manure balls. Can fecal transfaunation help alleviate the symptoms of ALL cases of chronic diarrhea or free fecal water syndrome? Absolutely NOT, but it might help some, and the risks and costs associated with it are low.

*The fecal transplant is placed through a naso-gastric tube.

Allow me to reverse course further for just a moment, to discuss alternatives to fecal transfaunation. Do you know what researchers recommend to cure most of these ailments? Forage change and pasture access (Mullen et al., 2018). So, let's not skip over that! Appropriate forage choices and pasture access are CORE beliefs at On Course Equine Nutrition, LLC. Also, according to the Equestrian Director of Cavalia who flew horses all over the world and experienced a lot of quarantine, much of the traveler's diarrhea was cleared up after the horses were re-exposed to herd mates (Personal Interview, June 16, 2022). Could be something about the solidarity and sterilization of our equine environments that increase a horse's risk of excessive diarrhea? Can pasture access with herd mates be a non-invasive cure to many of our horses' digestive problems?

I do need to dampen my enthusiasm for fecal transfaunation a bit more by sharing just how little we actually know about how it works in horses. I believe that Dr. Mullen and his team best summarized the use of fecal transfaunation in an abstract titled "Microbiota transplantation for equine colitis: revisiting an old treatment with new technology." Here is what the team concluded after studying four equine fecal transplantations at the Department of Clinical Sciences, College of Veterinary Medicine, Cornell University (Ithaca, NY 14853 USA).

"Although the clinical response was favorable in 3 of the 4 sick horses, microbiota transplantation did not cause the sick horses to adapt the microbiome of healthy donors as reported in humans following microbiota transplantation. The failure of the recipients to establish the fecal microbiome of the donor does not rule out the potential clinical benefit of the procedure. A large, randomized clinical trial is needed to better understand the impact of microbiota transplantation on equine health and the gastrointestinal tract microbiome."

The cautious efficacy statement above is supported by results in dairy cows. You might recall a transplant study from the article "Why Digestive Aids are Like Bits?" by OCEN, LLC. In that article, I explained how Cox et al. (2020) swapped the entire rumen content of cows and within 1-2 weeks the microbiome had returned back to the original hosts' microbiome. Isn't that INSANE?!? If you haven't read that article and the conclusions made by researchers, CLICK HERE.

Something that I've questioned about equine fecal transfaunation is the choice of donor made by researchers and veterinarians. In human fecal transplants, the human fecal donor is very carefully chosen based on four criteria; environment, immunity, diet and medications. With this in mind, perhaps the lack of donor specificity has contributed to the lack of success in equine fecal transfaunation. Obviously, I am not a veterinarian or researcher and this is NOT a scientific paper, but it's always good to ask questions!

  1. Environment- Do the donor and recipient share a similar space and thus similar stressors?

  2. Immune System Exposure- Are their immune systems fighting off similar pathogens. In human transfaunation, it's preferable that the donor and recipient share a bathroom. This is due to the assumption that they are exposed to similar viruses and bacteria, and that the donor is better at fighting off these pathogens.

  3. Diet Similarity- We might assume that diet similarity is the biggest priority, but in human fecal transfaunation, it's actually aspects of the immune system that are more highly prioritized. With that said, it could be beneficial for the host and donor to share the same haystack.

  4. Medications- The donor should not be on any medications that alter the digestive system microbiota.


There are some conditions that could warrant fecal transfaunation in horses, but it's important to have a thorough discussion with your veterinarian before considering.

  1. Known bacterial infections from Salmonella, Clostridium difficile or perfringens.

  2. Colitis that does not respond to medications like metronidazole, nutraceuticals like PrioBIos, BioSponge, and active yogurt cultures, or increased pasture access time.

  3. Continued use of antiobiotics and/or NSAIDS that lead to chronic diarrhea.

I am very excited to follow the research that is bound to arise from greater use of equine fecal transfaunation. I am emboldened by its accessibly and low cost as a treatment therapy. I've been shocked over the last two years, by how many horse owners contact me with this problem. The problem is real. Historically, veterinarians and nutritionists haven't had many tools in our toolboxes to consistently solve this problem. I know many professionals who have been defeated by chronic diarrhea many times no matter how many supplements were thrown down the horse's gullet. Let's face it...most of the time scoops of the latest and greatest supplement do NOT work. Sometimes, a significant forage change (change of NDF and ADF%) is our best bet, but that's not always the silver bullet either. Fingers crossed for some funding and researchers that have time and interest to explore fecal transfaunation further.

Additional Reading

  1. Read a fecal transfaunation case study from Swiftsure Equine and published online March 25, 2022. It's a great success story! CLICK HERE

2. Article on Horses Eating Other Horses' Poop: "Copraphagy Stands for GROSS" by OCEN, LLC, April 12, 2022

3. "Why Digestive Aids are Like Bits" by OCEN, LLC, October 11, 2021.


Cox, M.S., Deblois, C.L., and G. Suen. 2021. Assessing the Response of Ruminal Bacterial and Fungal Microbiota to Whole-Rumen Contents Exchange in Dairy Cows. Frontiers in Microbiology. 12:1386. Retrieved October 8, 2021 from

Custom Equine Nutrition, LLC. 2022. Free Fecal Water Treatment Flow Chart. Accessed June 16, 2022 at

Feary, D. J. and D.M. Hassel. 2006. Enteritis and Colitis in Horses. Veterinary Clinics Equine Practice. Volume 22:437-479. Accessed June 16, 2022 at Google Scholar.

Lindroth, Katrin. 2020. Free Faecal liquid in horses: Faecal composition and associations with feeding and management. Doctoral Thesis No. 2020:65. Faculty of Veterinary Medicine and Animal Science Acta Universitatis Agriculturae Sueciae. Accessed June 16, 2022 at Google Scholar.

McKinney, C.A., Bedenice, D., Pacheco A.P., Oliveira, B.C.M., Paradis, M-R., Mazan, M., et al. 2021. Assessment of clinical and microbiota responses to fecal microbial transplantation in adult horses with diarrhea. PLoS ONE 16(1): e0244381.

McKinney CA, Oliveira BCM, Bedenice D, Paradis M-R, Mazan M, Sage S, et al. 2020). The fecal microbiota of healthy donor horses and geriatric recipients undergoing fecal microbial transplantation for the treatment of diarrhea. PLoS ONE 15(3): e0230148.

Mullen, K.R., Yasuda, K., Divers, T.J., and J.S. Weese. 2018. Equine faecal micriobiota transplant: Current knowledge, proposed guidelines and future directions. Equine Veterinary Education. Volume 30(3):151-160. Accessed June 16, 2022 at Google Scholar.

Schoster, A., J.S. Weese and L. Guardabassi. 2014. Probiotic Use in Horses- What is the Evidence for Their Clinical Efficacy? Journal of Veterinary Internal Medicine. Volume 28:1640-1652. Accessed June 16, 2022 at Google Scholar.

Abstract Programme. The Eleventh International Equine Colic Research Symposium. July 7-10, 2014.

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