Tell me about success with transfaunation

Oh yes, this is where we are at.

Transfaunation comes at recommendation of internist at vet hospital (whom I trust completely) and my own vet team at home. It’s one of the few options left, other than steroids and exploratory surgery.

Objective is to reset digestive system with beneficial bacteria in the hopes of resolving continuing gas colics, potentially have a positive impact on 3 years of unending stomach ulcers, and maybe even IR.

Anyone have any success stories?

Curious if this horse has ever been on a regular program for Sand/Soil in the gut?
Wouldn’t hurt to try a weeks worth of Sand Clear/
I’ve noticed that much of our good hay imported from NE and Canada looks great to my eye but
both my horses insist on dunking it in their water tubs as they eat. Well it would amaze you what
is left in the bottom of their water tub each day when I empty it= at least an inch of MUD from the hay. We don’t have mud here in Florida. We have sand. But I’m careful how I feed and they never eat off the ground except while grazing the pastures which have good grass.
For the first time, this week I had one of mine act colicky, has had intermittent soft cow poops,
had a belly ache and stopped eating.
Just thought I’d mention this as Sand/Dirt/Soil in the gut can mess up their GI system.

1 Like

I’m having the same thing with alfalfa (latest batch I’m not sure where it was grown). One of my horses dunks his hay, all types, in his stall. I’ve been running “experiments” to figure out where is this mud in his dunking bucket coming from. It’s the alfalfa. I am arranging for a load of orchard and alfalfa from Indiana and Ky, I hope it’s not so full of dirt. I wasn’t having this issue when I had hay from out west.

1 Like

Worked on a human, our vet had regular surgery and while at the hospital caught C-Difficile and was in bad shape after they had to nuke her innards to get rid of it.
She was not rallying sufficiently on her own and they used properly prepared “donor fecal mixture” to try to get her digestive system back up to par. It worked.

Maybe that will help your horse?
Is common in dairies for cows with digestive troubles.

1 Like

I’ve floated manure in plastic bags to check for sand - nothing. I have done 4 days of psyllium (so far), and the good/bad news is that he’s going for 2 weeks to vet hospital tomorrow. They will do an xray to see if they see visible evidence of sand, and if so, will treat.


I know that it did NOT work for a lady in Canada whose horse has excessive smegma accompanied by an equally excessive odor.

My holistic vet offered it as a solution to the Fecal Water issue of one horse ONLY to see the expression on my face.:). His issue is resolved with an herbal compound from Dr. Xie’s product line. It addresses the functioning of the adrenal gland.

I personally would nix transfaunation and try the suggestions others have suggested. If those don’t work , find a holistic vet who is well versed in herbs and go that route.

I have had a handful of times where blood work didn’t show anything, the general vet(s) shrugged their shoulders, and the holistic vet (well versed in herbs & Chinese medicine) stepped in and solved the problems:)

1 Like

We have a female vet near me that gave up her ‘traditional’ vet practice and now does only
Holistic and man, is she busy. It’s fascinating what she prescribes. I haven’t used her but a friend did and really believed in what she did.

1 Like

My experience is 16-17 years old.

But years ago, I worked at a university where we would do this occasionally. Usually it was when a horse was stressed to the point they were completely off their hay and feed.

My non-scientific observation was sometimes it worked, sometimes it didn’t. But these horses were quite sick anyways, so it may have had nothing to do with the FMT procedure.

We did it a lot with other ruminants. We had a rumen juice donor and used her frequently.

I don’t think it can hurt anything but your bank account to try if your team recommends it… and it shouldn’t be an expensive procedure. You’re just tubing a horse and the microbes are, uh, free to collect from a healthy donor. :upside_down_face:


Ok, thanks for chiming in but there are no other suggestions that were offered yet other than checking for sand, which I have done. I have no idea why anyone would ever do a FMT for excessive smegma. That makes no sense to me but I wasn’t there and am not a vet.


I would spring for it. It’s cheap (vet visit cost more than the actual procedure). But do try to investigate the management too. Ulcers are almost always management.

I did it about six years ago on a horse we owned for 20 years, would do it again. Symptoms were rapid weight loss, colics (owned this boy for 20 yrs, NEVER had a colic), fecal water, completely runny manure, loss of interest in food. We pursued just about every diagnostic tool available to us: no ulcers, x-rays fine, nothing explainable. Tried him on metronidazole, improved for a week before tanking again. No improvement on Sandclear. The last ditch idea was to try transfaunation. He was much better within a few weeks. Still not 100% but better.

Vet’s best guess is inflammation (colitis) in his intestines disrupted healthy gut flora, and that “undigested matter” was further scraping and inflaming the gut.

For what it is worth, we later discovered he had Cushings about six months after the fact. He’s managed on pergolide but still occasionally will have runny manure. Good weight now though. He’s 27.

I’d investigate the ulcers. Has this guy been put on a 24/7 roundbale yet? I’m convinced that this is absolutely a “miracle cure” for ulcers – and way cheaper than two courses of Gastroguard. Even if you factor in purchase of Hay Hut.

Secondly, has he been turned out with a buddy yet? 24/7?

With persistent ulcers, if it’s not pain, it’s because the horse is stalled and isolated. Something to consider.


thank you for sharing your story!

My boy is at home, and always has been. Has always had hay in front of him, plenty of room to move around, and always a buddy in turnout. He’s very happy to come in at night when it’s cold, or during the day when it’s hot. He’s never alone, in or out. I’ve chased every rabbit hole for where he might have pain in his body, and resolved a few things. This latest round of colics (3) has been heart-stoppingly awful, so we are thinking it’s colitis.

I think it shows some promise, but there isn’t enough research on it yet and I think it does pose a few potential risks. I should mention that I am a microbiome scientist working in a very similar area, and I most likely wouldn’t have it done in it’s current state with one of my horses (I also won’t feed them probiotics but that’s another story).

  1. Most of the commensal/beneficial bacteria in the gut are obligate anaerobes. The process to do this involves collecting manure from a donor horse, straining it through cheese cloth and tubing it back to the horse. That will effectively kill all of organisms that you are trying to transfer. In the mean time, it allows blooms of facultative anaerobes (think E. coli - some of which is commensal some of which is not). There is research currently being done on this that I saw presented at a conference this fall but does not appear to be published yet.

  2. In horses, unlike people, there isn’t as much screening done for potential pathogens as there is in people.

  3. In an ill animal, you really run the risk that something you don’t want to colonize does - again, you are transferring good bacteria but also opportunistic pathogens. There are some proven cases where it seems to work - C. diff being the main one. But many conditions for which it does not.

  4. There is no guarantee that anything colonizes.

1 Like

Thank you - I appreciate your input.

I understand the protocol is the same as the one used at Tuft’s in their research; the donor horse is fully screened for adverse health issues before use. I get that there is no one and done … but my internist has had success with multiple days of treatment, and has recommended 14. l have found some confidence in a 2020 published study (linked below) that suggests the donor horse’s microbiome is replicated within the recipients after 3 treatments. I’m interested in your thoughts.

Also fascinated by the focus on a particular family of bacteria that, when overgrown, reduce pH and increase gas, and colic. And, while a longshot, not sure what other ways there are to re-set the gut bacteria. We have tried quite a bit so far with zero positive results.

“The bacterial community composition in horses with intestinal disease was substantially different from that of healthy horses. Horses with intestinal disease had fewer species and a less diverse bacterial population than healthy horses. The overgrowth of lactic acid-producing bacteria, such as Lachnospiraceae, Lactobacillaceae, and even probiotics for humans, can decrease the hindgut pH, which subsequently interferes with fermentation and produces excessive gas in the hindgut, eventually causing large intestinal colic. The abundance of methanogen, however, might be negatively associated with horse intestinal health.”

For what it is worth, ours was the same donor over several treatments. No cheesecloth was present. The vet quite literally showed up with a bag that had whole manure balls in it that he added warm water and some sort of solution to (I did not ask) before tubing it into the horse.

1 Like

Ok this is completely anecdotal. I had an OTTB stallion who was prone to gas colics. My vet at the time also worked at a standardbred farm and he suggested supplementing my horse with Vitamin A. The easy and relatively cheap source was Red Cell, one squirt per day.

It worked so well that I could tell when the barn neglected to inform me that it had run out because there was a gas colic within a couple of days.

Again, purely anecdotal and I’ve never looked for any research on the subject.

1 Like

There are certainly papers which show positive results (as you linked above), but there are also ones which show less promising results with similar preparation techniques (linked below). If you trust your vet, don’t let someone on the internet stop you.

There is certainly some evidence that humans can experience long term microbial changes after FMT, which is promising. At the same time, if the microbiome is indeed responsible all that we think it is, it’s also a weighty decision to choose an “ideal” donor. As mentioned, the preparation and screening is also much different for people but tbh horses eat each others poop all the time so it’s probably completely fine, and in pigs we literally just feed it to them and have good results. I also know that it’s done quite a bit in practice and it’s not like horses are dropping dead. Where I would be much more nervous would be a horse that was severely ill. I have linked some papers on this below.

With microbiome studies it is important to remember that most of the sequencing we do just gives us relative abundance. In the second study you linked the relative abundance of Lachnospiraceae was higher in horses with colic, however horses already have a huge amount of Lachnospiraceae, so did it overgrow or did rare taxa/ other taxa decrease making it appear to be more abundant? Interestingly in foals with diarrhea we usually see very low levels of Lachnospiraceae relative to healthy foals, and ponies typically have more than horses. It’s also a very important butyrate producing bacteria, which is important for intestinal barrier function and colon cell health.

Sorry if this is very rambley, it’s been a long week.

1 Like

Thank you!!! I wish I wasn’t the one driving today so I could read up on this … but I will later. Probably over dinner. HA!

The reason I pulled that one comment out about the lactic acid bacteria is that it just rings right for my horse who is suffering with painful gas colics, not diarrhea. His manure (pre/post) will be part of a larger study and I’d be happy to update you on him/it as I get information, if you’d like.

I mean, who isn’t interested in a full report on bacteria in a ball of poop??? :slight_smile:

Also, from your perspective, if you have thoughts about how to build/maintain a healthy biome, I’d love to hear them. I’ve tried quite a bit, which is why I’m at this place in the road, but it’s always good to learn more.

I’ve only seen it done in ruminates, which is a slightly different procedure. It helped most of them.

If you’ve done all the other things, (scope, X-ray abdomen, ultrasound abdomen, etc) I’m not sure why you wouldn’t give it a go. It’s cheaper and easier than an exploratory celiotomy. Less risk, too. And if seen more than one surgery still come up with nothing.

The only other thing I would mention, if you haven’t done anything to address the possibility of hind gut ulcers, maybe give that a go. Succeed has a program where they will give you back your money if you do the full treatment and it doesn’t help your horse.

In large dairies, with pictures:

1 Like