Severe Microbiome Dysbiosis – Seeking Feedback and Practitioner/Research Referral

[laurel]

I have documented severe gut microbiome dysbiosis through shotgun metagenomic sequencing: Proteobacteria at 79% (normal 1–5%), Enterobacteriaceae 72%, with near-total loss of beneficial bacteria like Faecalibacterium and Akkermansia. SCFA production is severely impaired, and barrier dysfunction (“leaky gut”) is evident.

This is in the context of long-standing seropositive rheumatoid arthritis with erosive disease. I have failed all conventional biologic DMARDs, but helminthic therapy has restored much of my function. The dysbiosis, however, remains extreme.

I am seeking (a) you thoughts, and (b) referrals to a clinical research center or specialist with direct experience in microbiome restoration at this level of dysfunction. Standard gastroenterology and functional medicine approaches have not been helpful. If you know of any academic or translational programs taking cases like this, I would appreciate leads.

 

[Michael Harrop]

It sounds like you didn't read this yet: https://forum.humanmicrobiome.info/threads/before-you-post-or-comment-here-please-review-the-testing-page-of-the.24/

You could start next with the FAQ: https://humanmicrobiome.info/faq/

There are no "microbiome specialists" who can solve your problems. FMT is the solution and it's not available: https://forum.humanmicrobiome.info/threads/the-fda-and-fmt-regulation-part-2-jul-2024-humanmicrobes-org-i-met-wit.520/#post-1370. You'll have to read through that thread and get involved.

 

[SFBayFMT5]

Michael is right, aside from practitioners who perform re-seeding of the microbiome with organisms from a healthy gut, i.e. FMT, microbiome treatment isn't really a thing that has results to show for it. Functional medicine practitioners use the gut as kind of like a marker that shows whether "something" is wrong, but then have nothing to actually do about it aside from what they are already doing otherwise (vitamins and minerals, herbs, healthy diet and lifestyle, killing outright pathogens with antibiotics sometimes (this is "good" in that unlike herbs and dietary changes, these can actually have dramatic effects in the short term--however at the same time it's "bad" as you further deplete what you have too little of at the same time).

It appears you have what I would consider "classic, colonic" dysbiosis. By that I mean that this is the picture that much of the research on the gut has been about... which puts you in possibly a better place than people like myself who don't have this sort of severe depletion of usually common species at the expense of Proteobacteria (I had < 0.1% Enterobacterales and ZERO Enterobacteriaceae when my symptoms were at their worst, which is effectively the opposite picture). Most of my issues are likely small intestine related.

Considering that the species you are lacking are common in the typical gut anyway, I suspect that FMT from almost ANY reasonably "normal" donor would reduce your dysbiosis at least "on paper"--whether that would also treat all of your symptoms is an open question.

 

[EpilepsyFMTcure]

There's a company that makes akkermansia now if you're looking to supplement that. I drink a TON of kefir, like, a TON, and that's helped me a lot. I believe the company that makes akkermansia also makes a few other SCFA bacteria strains in supplement form. I've had mixed results with them, but I believe (can't prove) that before supplementing them I didn't have any at all.

 

[SFBayFMT5]

EpilepsyFMTCure, which of the SCFA bacteria strains helped you and which didn't?

 

[EpilepsyFMTcure]

EpilepsyFMTCure, which of the SCFA bacteria strains helped you and which didn't?

Click to shrink...

I've tried akkermansia a few times, and one of those times I got the mixture where they also have Clostridium butyricum (and others), and that one I felt like actually helped pretty quickly. I want to say it was "glucose control." My experience with the akkermansia alone actually seemed at first like it was making my gut and epilepsy slightly worse, but I believe that to be a sort of herxheimer reaction. Akk. breaks down biofilms, so I think it was releasing a LOT of the klebsiella p. into my gut and destroying it, which would cause gut inflammation/leaky gut basically, kind of like an allergic reaction.

Over time though I think it's helped, like, long term. I might try another round of akkermansia if I still have any left. What I was doing is buying one bottle at a time, and I'd run through a bottle, then rest for about a month, then do another bottle, that was basically the routine I did for six months. But like I said I felt like the glucose control one (which has a few other strains in it other than just akk and clost buty) was the most effective. To be clear, this wasn't a cure for me, but my epilepsy is MUCH more controlled now than it was before I tried those and based on how low my akk levels were beforehand I don't think I had ANY akk before introducing it myself. I can't say for sure it was those that actually changed things either because since then I've also tried keto a few times (absolutely didn't work for me, made it MUCH worse, klebsiella p. actually thrives when there is less fiber because the other fiber fermenting strains it competes with die off). I guess the upside is that its very obvious to me my gut is so obviously the cause of my epilepsy, and can be modulated by manipulating it. Below is the link to the one I think provided the fastest and most efficient help, but I'm not trying to shill for them. I know a girl that tried akk and had some negative gut reactions because of it, nothing lasting or serious, just indigestion, but she had a normal gut beforehand and she shouldn't have taken something she didn't need.

https://pendulumlife.com/products/pendulum-glucose-control-probiotic-blood-sugar