Fecal Microbiota Transplant (FMT) for Pouchitis – My Experience

It has now been over two years since my experience with FMT, and I have still neglected to document it in any way. This is just atrociously bad n=1 experimentation protocol on my part, and kind of speaks to how tapped out I was by The Great Search for Answers. I think the effort I went through to find/secure a part in/complete the FMT trial was all I had left in me at the time, so after it was over, I entered a phase of Staunchly Ignoring The Problems. Which was honestly very necessary. Sometimes ya just gotta take a break, you know?

But I owe it to my future self and the general knowledge bank of the internet to document and share what I can, so here we are! If you just want the cliff notes/what I learned (hint: there’s one exciting thing!), scroll to the bottom. Because per usual, this became way longer and more rambling than necessary.


Why FMT?

I go into more details about the early part of my story here, but essentially I was diagnosed with ulcerative colitis when I was 14, tried a bunch of stuff, none of it worked, and had my colon removed when I was 17. It sucked, and definitely didn’t “cure” my UC, so I’ve still been plugging away at trying to figure things out since then.

The main concerning issue (from a long-term health/avoiding cancer and other bad things standpoint) that I’m trying to address is that I’ve never really gotten my inflammation under control, and still have intestinal bleeding. But the other more functional issues (like bloating, competing with geese for number of daily poops) would be great to improve too.

Unfortunately FMT research didn’t cross my radar until after I lost my colon, but since repeated stool tests have confirmed that my gut bacteria are wack, I figured it would be an interesting thing to try. Problem was, I wasn’t willing to DIY this particular treatment, since it wouldn’t be possible to do as much testing on the donor as I’d like, and my understanding is that it’s best to keep the implant material in anaerobic conditions, which isn’t really possible in an amateur DIY setting.

So the only other option to get an FMT was to join a clinical trial, which would have been easy when I had UC, but without my colon, I was not eligible for any FMT studies. That is, until the fateful day when I found a trial studying FMT in pouchitis – and it was accepting participants!


WTF is pouchitis?

For those that don’t know, pouchitis is the extremely stupid name for the extremely common condition where the j-pouch becomes inflamed. A j-pouch is the little poop reservoir that surgeons create from the end of one’s ileum after removing one’s colon. So basically, pouchitis is just ulcerative colitis except now in your new fake colon instead of your old real colon. Ain’t that grand?

Anyway, I found this study specifically targeted at people who had undergone the same surgery as me. But there was still an issue with eligibility, because even though I knew without a doubt based on my symptoms that I had pouchitis, it hadn’t been confirmed via scope.


Getting into the study

In my first year or two after surgery, I had many a scope (“pouchoscopy”) done in an effort to determine why I was still bleeding. But weirdly, it never showed pouchitis. The pouch itself looked mostly healthy – there was just a small ulcerated area around the suture site that was continuing to nonchalantly bleed for no apparent reason. So, no pouchitis diagnosis. Eventually, I stopped consenting to scopes, because I didn’t feel the need to have cameras repeatedly stuck up my butt in order to have the doctors repeatedly tell me the same thing.

Fast forward another year or two, and things had gone downhill a little. I know my body pretty well at this point, and I would’ve bet some serious money that I now had diagnosable pouchitis, but unfortunately, I still had to get scoped in order to get the diagnosis in order to join the clinical trial.

So, I got scoped again. There was a fun little conflict of interest with myself in the weeks leading up to the scope, wondering if I should deliberately sabotage my poor pouch’s health, just to make sure. I can’t remember exactly what agreement I reached with myself, but I definitely wasn’t particularly nice to my gut during that time. Outcome? Very significant pouchitis. So I guess that was a success.


The Protocol

Anyway, many (many) phone calls and forms later, I was officially part of this trial. The protocol was as follows:

1. Take rifaximin for five days

2. Wait three days

3. FMT #1 administered via pouchoscopy

4. Wait at least four weeks (in my case, this ended up being more like four months due to scheduling conflicts)

5. FMT #2 administered via pouchoscopy

6. Optional capsule therapy, where you swallow FMT capsules once per week for six weeks (I opted in)

Here’s a link to the study info page, if you want to check it out.

(Side note: I live in NC, and the trial was at UCSF in San Francisco, so being part of this trial entailed one two-week visit to SF, and one two-month visit. I had just graduated from undergrad when I enrolled in the study, and the two-month visit basically meant that I couldn’t get a real job until after it was over, which ended up being in MARCH of the following year. I feel like I deserve points for that level of commitment.)


Rifaximin – underwhelming

I had been almost as excited for the rifaximin portion of the treatment as I was for the FMT, because I’d wanted to try a course for a while, but didn’t want to put myself through the doctor-related trauma necessary to get a prescription. So even though five days isn’t a hugely long course, I was hopeful that maybe I’d see some symptom improvement before I even got the FMT.

Instead, as usual, my body was like “oh, were you talking to me?” I didn’t even get the die-off symptoms that I normally get with any type of intestinal ecosystem-shifting intervention. I was tired and didn’t get out of the house much that week, but that was unfortunately pretty characteristic of me at the time.


FMT #1 – definitely did something

The procedure itself went smoothly, and I managed to hold the FMT in for around 4 hours afterward.

Later the same day, I had weird draining from my right eye and nostril, then some pretty intense achiness and a low fever for the next ~3-4 days. (Fever may have been high at points; it was just low when I got the chance to measure). I also noticed increased pouch achiness and urgency, and had to get up at least four times per night to use the bathroom instead of my usual 1-2.

I continued not feeling great in the weeks after the FMT, but I also had a lot of other things going on in my life that were not ideal, so I can’t pin everything on the FMT.


FMT #2 – uneventful

I went back to San Francisco in January 2017 for my second treatment. The treatment itself went about the same, but interestingly, I didn’t get a die-off reaction like I did with the first treatment, and also didn’t have worsened gut symptoms. So it definitely seemed like anything the FMT was going to do for me had been done by the first one.


Capsule Therapy – a little too eventful

This is where things get kind of interesting. One week after my second FMT, I began the optional capsule therapy portion of the study, which entailed visiting UCSF once per week to swallow ten capsules containing FMT material. (Yeah, yeah, gross, yuck. Just don’t think about it too hard.) If I recall correctly, this was always done first thing in the morning on an empty stomach, but I’ll need to double check on that if I can get in contact with the study coordinators again.

A few hours after swallowing my first batch of capsules, I started feeling nauseous, and eventually was sick to my stomach. This happened the second and the third week as well, like clockwork, so at that point I decided to/was forced to discontinue the capsule therapy, and that was the end of my study treatments. I’ll spare you the details, but the reaction each time was drawn-out and absolutely miserable.

What I found interesting, though, is that I didn’t start feeling sick until at least an hour or two after taking the capsules. And by the time I actually threw up each week, the capsules were already well out of my system in the other direction (I’m trying so hard to avoid TMI here you guys). So it’s not like my body was trying to get rid of the capsules before they could progress through my digestive tract. Or if it was, it did a shitty job (heh).

Also, I’m pretty sure the capsules were enteric coated, so they shouldn’t have dissolved until leaving the stomach anyway, although I obviously can’t confirm what actually happened in vivo.

The study coordinators didn’t really have any thoughts to share with me as far as why this happened, and I didn’t get the sense that this was a common reaction. Congrats body – more weird points for you!

Assuming that the capsules didn’t dissolve in the stomach, the reaction would have to have been caused by something that happened below the stomach, but above the j-pouch where the pouchoscopy-delivered FMT couldn’t reach. I do sometimes feel nauseous with die-off reactions, so it’s not unprecedented, although it’s never been this severe.

But perhaps the bacteria in the FMT interacted with bacteria in my small intestine in such a dramatic way that it just caused a more severe die-off reaction than what I normally have. But then, I would have expected some other die-off symptoms (achiness, headache, other cold/flu symptoms) to also happen, and to stick around for a day or so. But I always felt mostly back to normal the next day, albeit pretty wiped out. So at this point, I really don’t have a good theory as to what that was all about.



Overall, my gut symptoms remained more or less unchanged (boo). But there was one very significant (in my opinion) result, and I’ll go ahead and share some of my lab values too.

The Plesiomonas shigelloides story

So the very significant result is that the FMT seems to have finally gotten rid of a pathogenic bacteria called Plesiomonas shigelloides that I’d had since at least 2013, maybe before, that I hadn’t been able to get rid of with anything else. According to the internet at large and all my doctors, Plesiomonas shigelloides infections are self-limiting and don’t typically require treatment. (Think your basic bacterial gastroenteritis, like when people get diarrhea for a few days after eating something weird.)

A recent-ish review on the current P. shigelloides happenings mostly corroborates this. The authors do say that it is “an infrequent but recognized cause of chronic diarrhea,” but guess what “chronic” means in this case? Two weeks to two months. TWO WEEKS to TWO MONTHS. We’re talking three YEARS at least, maybe longer, that I’ve had this infection. Cool.

So anyway, since my GI doctor wasn’t “comfortable” (??) trying to treat this infection, I worked with a functional medicine doctor to do an intensive herbal/”natural” antimicrobial protocol. The antimicrobials we used were:

  • GI Synergy (a bunch of herbal antimicrobials)
  • Lauricidin (monolaurin)
  • A-FNG (more herbal antimicrobials, now in liquid form for optimum nastiness)
  • InterFase Plus (biofilm disrupter – enzymes + EDTA)

Pretty solid, right? Here’s my stool test results prior to doing this protocol:


Aaaand here’s my stool test results AFTER the protocol:


Whomp whomp.

I mean, you can definitely see some improvement. But that Plesiomonas shigelloides is still j chillin’. Super unconcerned about the war we just waged on it.

Fast forward to September 2016 and the FMT trial. They did a bacterial stool culture just prior to the course of rifaximin, and unsurprisingly, my Plesiomonas shigelloides buddies were still hangin’ out.


BUT THEN, in the follow-up stool culture in January, after the rifaximin/FMT…the Plesiomonas shigelloides was GONE. 



And confirmed again in March:


So that, by far, was the most significant result from this whole ordeal. Maybe the crazy reaction I had to the first FMT was all the Plesiomonas shigelloides being killed and leaving my body in a very dramatic fashion.

(Side note: the P. shigelloides first showed up in a stool test several months after The Great Garlic Experiment of 2013, wherein I ate horrifying amounts of raw garlic for many days in a row in an effort to treat self-diagnosed SIBO and fix all of my digestive woes. Unfortunately, the results of the Great Garlic Experiment of 2013 were exclusively bad.

But this means that either 1) I had P. shigelloides before the garlic, and the garlic did not kill it; or 2) I acquired P. shigelloides sometime during the ~6 months between The Great Garlic Experiment of 2013 and the stool test, perhaps due to me having left open a gaping hole in my intestinal ecosystem where pathogenic bacteria could take root. Either way, interesting to note.)


Bloodwork Results

My labs don’t show anything super interesting.

FMT lab values chart

It is kind of strange that my fecal calprotectin skyrocketed, while my CRP and Sed rate both went down. All are markers for inflammation, so normally they would tend to go up/down in concert.


Cliff Notes

  • Did a course of rifaximin, then two FMTs spaced four months apart
  • Got a die-off reaction from the first FMT, but not the rifaximin or the second FMT
  • Also did tried to do an optional part of the study that was six weeks of FMT capsules, but had a weird bad reaction to them and had to drop out after three weeks
  • No noticeable improvements in symptoms, digestive or otherwise
  • Stool tests showed that the rifaximin and/or first FMT got rid of a pathogenic bacteria called Plesiomonas shigelloides that I’d had for years and hadn’t been able to get rid of, which is super nifty

So there you have it. The long, rambling saga of my experience with FMT, as remembered two years later because I suck. But better late than never, right?

If any of you have ever experimented with FMT, I’d love to hear about your experience!


3 Thoughts on “Fecal Microbiota Transplant (FMT) for Pouchitis – My Experience

  1. Hey! I just started my DNA appliance or “palate expansion appliance” (I think there are some legal issues with Dr.Singh, from what I was reading on google). How long did you use the appliance??

    • Hey Calvin! I started with the basic expander in January, and then switched to the DNA/meridian in May, but stopped expanding it sometime in July, and have just been wearing it at night ever since as a sort of retainer without increasing the expansion. My post from September is pretty much still where I’m at, update-wise.

      • Did you have any noticeable results in that period of time? Also, are you trying to correct an arched palate? I noticed you said your teeth had been pushed a little to far from the bone. I have a vary high arched palate. Hoping this will finally correct it.


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