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Alyssa Luck

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Fecal Microbiota Transplant (FMT) for Pouchitis – My Experience

Alyssa Luck · Dec 7, 2018 · 3 Comments

Last updated April 23, 2022.

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 (there’s one exciting thing!), scroll to the bottom. Because per usual, this became way longer and more rambling than necessary.

Table of Contents
Background
        Why FMT?
        WTF is pouchitis?
        Getting into the study
The protocol
        Rifaximin: underwhelming
        FMT #1: definitely did something
        FMT #2: uneventful
        Capsule therapy: a little too eventful
Results
        The Plesiomonas shigelloides story
        Bloodwork results
Cliff notes

Background

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.

Results

Overall, my gut symptoms remained more or less unchanged (boo). But there was one significant 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.

October 2013

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 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. 

!!!

I had another stool test a couple months later in March (this time the same type as the first two, Doctor’s Data). Still gone, baby!

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 created a gaping hole in my intestinal ecosystem where pathogenic bacteria could take root. Either way, interesting to note.)

Bloodwork Results

Here are my results for fecal calprotectin, c-reactive protein, and sed rate before and after the FMTs:

Before (September 2016):

After (January 2017):

It’s interesting to me that my fecal calprotectin increased significantly, while my CRP and sed rate both went down. All are markers for inflammation, so I would’ve expected them to go up/down in concert.

I’m sure there’s an explanation, and maybe even quite an interesting one, but I haven’t taken the time to try to analyze these results.

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?

Related

Microbiome Optimization for IBD fecal microbiota transplant, fecal transplant, pouchitis, ulcerative colitis

Reader Interactions

Comments

  1. Calvin says

    December 16, 2018 at 7:26 pm

    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??

    Reply
    • Alyssa Luck says

      December 17, 2018 at 9:44 am

      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.

      Reply
      • Calvin says

        December 17, 2018 at 1:01 pm

        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.

        Reply

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Hi! I’m Alyssa. I like thunderstorms and cats, hate wearing shoes, and enjoy devising extensive research projects for myself in my free time. This is me in Bali with a monkey on my shoulder. And this is my blog, where I muse about health-related topics and document my relentless self-guinea pigging. If you want to know more about me, click here!

alyssa.luck

alyssa.luck
Photo dump from the last year. Thanks to everyone Photo dump from the last year. Thanks to everyone who made 28 the best yet - excited for 29🥰

(PS. In case anyone wants to know what it’s like in my head, I was going to write something like “year 28” or “my 28th year” but then I realized that the year between your 28th and 29th birthdays is not your 28th year of life, it’s your 29th year. I am turning 29 because I have been alive for 29 years. So then I had a whole thing about how to word it without being inaccurate and ended up going with what you see above which is vague and weird but the point is it was a good year and I love all the people in my life dearly)
Biology of Belief (2005) was written by Bruce Lipt Biology of Belief (2005) was written by Bruce Lipton, who earned a PhD in developmental biology in 1971 and was an anatomy professor and academic researcher in the 70s and 80s. Despite the book's presentation and Lipton's background, this is not a science book. It is an exposition of an ideology, supported by haphazard and poorly contextualized nuggets of evidence, rhetorical leaps, and a mind-boggling overuse of analogies. 

The book largely failed to deliver on its promised content. What it does is argue for the primacy of the environment over DNA in controlling life; propose that the cell membrane rather than the nucleus is the "brain" of the cell; invoke quantum physics to explain why modern medicine fails; explain that our behavior is largely controlled by our subconscious mind; inform parents that they therefore have a great deal of control over the destiny of their children; and conclude that humans must become nonviolent protectors of the environment and of humanity because Everything Is Connected.

It’s not that these points aren’t relevant to the topic at hand - they are. But they were not connected in a coherent way that would explain how “belief” actually works (like…biologically), and the treatment of scientific concepts throughout was careless, or perhaps disingenuous.

I think he's correct about many things, some of them being common knowledge. For instance, the "new" science of epigenetics is now old news, as is the critical role of parenting and early environment in shaping a child’s future. But however important these and attendant concepts may be, the book did not do a good job explaining, supporting, or connecting them. 

As far as practical guidance, he refers the reader to a list of resources on his website, which is fine, but I expected some scientific insight into how/why those modalities work. None was given. 

On the plus side, the book was quite thought-provoking, and I came away with loads of references and topics to follow up on. My favorite line? "There cannot be exceptions to a theory; exceptions simply mean that a theory is not fully correct."
Friedrich Nietzsche, The Gay Science (section 382) Friedrich Nietzsche, The Gay Science (section 382), as quoted in the introduction to Thus Spoke Zarathustra because I like the translation better.
This paper totally changed the way I think about e This paper totally changed the way I think about early nervous system development and the relationship between physiology and sociality. 

The authors propose that newborn babies are not inherently social, and have just one goal in life: physiological homeostasis. I.e. staying alive. This means nutrients, warmth, and regulation of breath and heart rate, i.e. autonomic arousal (it’s well-accepted that newborns sync their breathing and heart rate with caregivers through skin to skin contact). 

All these things are traditionally provided by a loving caregiver. So what the baby experiences during the first weeks of life, over and over, is a shift from physiological perturbation to homeostasis (a highly rewarding event inherently) REPEATEDLY PAIRED with things like the sound of a caregiver’s voice and seeing their face. Thus, over time, the face/voice stimuli become rewarding as well. 

The authors argue that THIS is the beginning of humans’ wiring for sociality, and may explain why loving social interactions can have such a profound regulating effect on physiology throughout life: because the brain was trained for it at an early age. 

This framework holds all kinds of fascinating implications for what happens if that initial “training” isn’t so ideal. What if the return to nutritional homeostasis via feeding is paired with negative expressions and vocalizations rather than loving ones, perhaps as could occur with PPD? What happens if the caregiver has poor autonomic regulation, such that social stimuli become paired with cardiorespiratory overexcitement in the baby? Could that have potential for influencing later introversion vs extroversion? (Because if social interaction is paired with autonomic overexcitement, that could lead to social interaction literally being more energetically draining, which is what introverts experience. Thoughts?)

For my energy metabolism enthusiasts: Table 1 in the paper draws a link between metabolic rate and sociality across species. Swipe for a screenshot. 

Anyway, check out the paper! It’s free, just google “growing a social brain pdf.”
I’ll be under general anesthesia in a couple day I’ll be under general anesthesia in a couple days to have two tooth implants placed, and I think I’ll take the opportunity to have a little heart-to-heart with my subconscious mind. A bit of medically-assisted self-hypnosis, if you will. 

I randomly stumbled upon these papers a couple months ago - an RCT showing reduced post-op pain in patients who listened to recorded positive messages while under general anesthesia, plus a post-hoc analysis of the same data that found reduced post-op nausea and vomiting in a subset of high-risk patients. 

The full review paper from the first slide is unfortunately in German, but it has long been recognized that even when unconscious, the patient is listening (for better or for worse). 

It boggles my mind that it isn’t standard of care to have patients listen to recordings like this while under sedation, considering that almost nothing could be easier, safer, or cheaper, and we have at least some evidence of significant efficacy. I mean c’mon, what more could you want from an intervention? 

(Yeah, I know. Profit. If anyone still thinks that our medical system operates with patient well-being as the foremost goal, you’re deluding yourself.)

“There should be a fundamental change in the way patients are treated in the operating room and intensive care unit, and background noise and careless conversations should be eliminated.”

“Perhaps it is now time to finally heed this call and to use communication with unconscious patients that goes beyond the most necessary announcement of interventions and is therapeutically effective through positive suggestions. When in doubt, assume that the patient is listening.”
If you've seen "vagus nerve exercises" that have y If you've seen "vagus nerve exercises" that have you moving your eyes or tilting your head, you've probably encountered the work of Stanley Rosenberg. The exercises he created and introduced in his 2017 book now appear in instructional videos all over the internet. 
 
The book itself has much to recommend it: it's accessible, it's practical, it's inspiring. But it has one major flaw: the solid practical and informational content regarding the cranial nerves is framed in terms of the scientifically dubious polyvagal theory. 
 
I particularly enjoyed the book as an introduction to the therapeutic arena of bodywork, of which Rosenberg is a skilled practitioner. His book is full of case reports that demonstrate how immensely powerful extremely subtle movements and physical manipulations can be. These do need to be kept in perspective: it's a small sample size of the most remarkable cases, and the results were achieved within the supportive clinical environment of a skilled practitioner. You can tell from his descriptions how refined his technique is. But nevertheless, it was a paradigm-shifting read for me, and the exercises give you something concrete to play around with. 
 
The book also brought the cranial nerves and the concept of “social engagement” to the fore as arbiters of health. Rosenberg has a solid background in cranial nerve anatomy and shares many interesting tidbits and considerations that you don’t typically hear; for instance, the potential impact of dental and orthodontic work on cranial nerve function.
 
So, is it worth reading? If any of the above piques your interest, go for it! Just read my post on polyvagal theory first – you can use the book to practice separating the wheat (solid informational content) from the chaff (pseudoscientific framing). If nothing else, the book is a nice reminder that genuine healers who get lasting results for their patients do exist.

But if you just want to try the exercises, you can easily find them all on YouTube. 

“You learn techniques to understand principles. When you understand the principles, you will create your own techniques.” -Stanley Rosenberg
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