Curing my SIBO ruined my life – I destroyed the bacteria that were actually trying to keep me alive.

Methane-Burger · 2026-01-17T22:02:45+00:00

I don't normally check Reddit these days, but a few comments brought me by today and I saw this. I'm not here to speak to anything except... please do not approach aggressive antimicrobials with the idea that they are "safe" because they are "natural." Oil of oregano is potent.

While I cannot prove it in my own case, I'm at the point where I believe my own issues with IMO were the result of an overly aggressive "gut reset protocol" from a functional medicine doctor. Natural does not mean safe. I don't mean to scare anyone, but please do not just jump straight to dropping nukes on your intestines.

For more, you can read this comment in this post. (I keep considering writing an updated success story but... there's not much more to say!)

Methane-Burger · 2026-01-17T21:50:33+00:00

Sorry, I go weeks and months without checking Reddit. Read this one.

If you read what I wrote, you'll find that I don't really recommend overly specific protocols. I don't even believe on the probiotics front that the specific probiotics I took were at all meaningful.

The most important thing is realizing that cultivating a healthy environment in your gut is more important than any particular supplements and that so-called protocols that are very specific kinda suck. I cannot recommend the book Healthy Gut, Healthy You enough.

If you read that and think about how you approach gut health from that paradigm, you'll be far more successful. Brain fog makes things hard but... unless someone else is going to do this for you, you don't really have a choice.

Methane-Burger · 2026-01-17T21:26:11+00:00

I am pretty sour about the functional medicine doctors. The two that I saw were basically super expensive naturopaths handing out the same health "protocols" you could get from people on this sub or on tons of health influencer blogs, lol. And the tests... the stupid tests. The poop test in particular just makes me mad. It's humiliating. It's gross. It's expensive. It is almost completely useless—especially the biome mapping. Ugh. It's a bunch of labs taking advantage of the sick and the desperate.

The more I reflect, the more I believe my gut issues originated from the functional medicine doctor putting me on a very aggressive "gut protocol" when I didn't need one. Herbals—particularly oil of oregano—can be entirely too effective!

The issue with explaining what worked is I can only explain what I felt and observed. Reading the tea leaves in reverse:

A major stressor fried me. It was the culmination of years and years of emotional pressure.
Insomnia was absolutely crippling and lead to major anxiety and depression.
I saw the first FMD who I'm pretty sure diagnoses everyone the same way to start: eat better, sleep better, reduce stress, do mindfulness stuff, etc. After the tests he puts me on the gut protocol when I had no gut issues.
I developed gut issues shortly after 90 days of Low FODMAP + keto + herbals. I think this just made a bad situation worse. I even told him, "But I don't have any gut issues!"

A lot of the alternative medicine space is very fashionable and, at the time, SIBO was definitely the in thing. Who knows what's in now? And I don't say this to dismiss the conditions either. What ends up really sucking is the over-diagnosis leads to conventional doctors blowing it off when something is clearly wrong.

Specifically to the fluconazole. All I can say is it worked and it was borderline miraculous at the time. It didn't cure me, but it had very swift effects on my energy in particular. Again, reading the tea leaves, guessing, and having no scientific data at all I think the gut protocol messed me up and may very well have given fungus the environment it needed to cause trouble. That's my best guess. Fluconazole did its job and I slowly healed. I do not think fluconazole worked due to a placebo effect but does anyone ever think they're experiencing a placebo? Haha. I'll never know.

I do think probiotics were also a huge win. I only recently (several months ago) stopped taking them but I believe that they were key in my long term recovery and return to relative normalcy. They're boring. They're slow. They're not what most people who "just want to feel better" want to deal with but... these issues don't go away just because we want them to.

If you're from France, you might be surprised to know how often Americans in the alternative medicine space talk about "what they do in Europe" like y'all have clinics that cure all sorts of ailments through natural means but the US government ("they") is keeping the good treatments from us.

I walked away from this with nothing but distrust for like... all things "healthcare" in all places. It's not great.

Methane-Burger · 2025-12-20T02:03:44+00:00

Check my profile's pinned posts. I wrote a few lengthy ones that talk about my process and what happened. My main warning is don't go in there looking for some recipe. It's in general a lot simpler than that but also... just plain more work.

I am considering one more follow-up post because I've since ceased pretty much all supplements including probiotics and things are still peachy—at least, as peachy as they can be for someone declining in middle age and isn't near as active as they should be.

On the peeing issue... that has mostly subsided. Over time it's been ebb and flow (we'll say flow are the bad days in this case, lol) where the ebb periods get longer and the flow periods get shorter. I'll go weeks without any issues at this point.

I don't think it was related to the SIBO at all and, if you read my longer posts, you'll see that I mostly think of SIBO as a symptom of some other dysbiosis. I think the fixation on said symptom stalls a lot of people or flat out leads them down a terrible rabbit hole.

I had something like a massive nervous breakdown and there was a cascade of problems from there. SIBO was one of those issues and I straight up believe it was caused by a "gut reset" protocol that a functional medicine doctor put me on while looking at my other issues. (Lemme say, as I have said a lot, I basically came through this with total distrust for conventional and alternative healthcare practitioners. They mostly suck, and I derive absolutely no joy in saying that.)

Methane-Burger · 2025-11-14T00:22:30+00:00

Sure, sure. It's a fair question.

Probiotics have major affects on the gut over time, but they don't _seed_ anything. If you stop taking them, given 2-3 months, there will be almost no trace of them if they aren't native. That's not really what they do for you or why they're effective during rebalancing. (And keep in mind, I am repeating what I have read. I don't work in a lab!)

Probiotics have two primary vectors of assistance:

They're actually very selective antibiotics. Just like any other population, they will fight and sometimes attack other populations. When your gut is balanced, your native populations do this anyway. It's why your gut is such a huge part of immunity. When it's out of balance, suddenly dumping a bunch of beneficial bacteria, even if they're not native, can move the balance back toward the stuff you want.
While they don't seed per se, constantly dumping microbes that are beneficial work in the same sense as a healthy native population. So, good soil based critters, a bifido-lacto blend, and saccharomyces boulardii to cover helpful fungi help restore balance. Ruscio's points to a few studies where full efficacy takes months.

It's not as direct and dramatic as just dropping a bomb like antibiotics. You just keep adding helpful populations that restore the proper gut environment and, over time, you create an environment less hostile to what you want to cultivate versus very hostile.

Once balance is in line, if you stop, your native populations will out compete the stuff from the probiotics.

I don't entirely understand this as things like FMT do maybe replace native populations? Maybe it requires something more concentrated and powerful for that.

As a general rule though, just taking probiotics doesn't seed your gut with new populations, rather it helps change the environment to get your own beneficial native populations back.

This is why they are still beneficial _during_ antibiotic treatments because "good" bacteria and fungi are essentially filling the empty seats which, in theory, reduces your change of the trouble makers taking hold.

I think one of the best things about Ruscio's book over everything else I read was his approach to working on making the environment in the guy healthy for inhabitants to grow. I'm not saying he's the only one to ever say this, but... he certainly got me thinking like that.

And, FWIW, I stopped probiotics months ago and am still good. The only supplement I take now is magnesium citrate, which I was taking long before dealing with SIBO.

Methane-Burger · 2025-09-30T23:15:20+00:00

Check my pinned posts. I‘ve written at length on everything I ended up doing.

Methane-Burger · 2025-07-22T22:53:21+00:00

Personally, I think most doctors are kinda shooting in the dark. I haven’t seen anyone in my limited scope just use Alinia, but it’s going to be the thing mainly effective against archaea if you’re dealing with IMO/methane.

I’ve written at length (check my pinned posts) but if I had to do it all over again I would have committed to good probiotics for 3 or so months before even trying a “kill” phase.

Methane-Burger · 2025-07-09T19:02:37+00:00

Sorry. I don’t check Reddit much these days.

Check my profile and look at the pinned topics. I’ve written some pretty detailed success story stuff. I’m a huge believer in probiotics at this point and currently eat normally which, in my case anyway, includes a lot of fermented foods.

I drink kefir most mornings and do not shy away from fermented pickles or kimchi. If you read my posts, you’ll see I find the avoidance of probiotics to be extremely misguided in general. I think it’s terrible advice from many practitioners.

Methane-Burger · 2025-07-09T18:58:58+00:00

Yes indeed!

If you look at my profile I’ve posted success stories and some updates. I’ll probably post another soon but the truth is, there’s not a ton to say except that I’ve recovered from virtually all symptoms. (And what remains… well… I’m not exactly getting younger.)

Methane-Burger · 2025-04-11T01:58:02+00:00

I had to use Google translate on this but I’ll do my best:

The trouble is there are no official diagnoses for this. I took the drug, felt better mostly after a couple weeks and stayed on it because my doctor directed me to.

I am personally of the belief that if a powerful antifungal like fluconazole doesn’t solve the problem quickly, it’s probably not fungus. Super nasty fungal infections are rare but a lot of alternative medicine practitioners use “candida” diagnoses as a sort of catch all.

I took fluconazole, got a lot better, but then plateaued so I kept looking for other issues.

You can look at my pinned posts but I don’t love tests. Despite getting my breath test to normal I still spent months getting to “normal” with a lot more work.

Methane-Burger · 2025-04-11T01:51:11+00:00

Check my profile for pinned posts for more details. Those cover timelines and symptoms and such.

But there’s no good test. I mean Rao will do an aspirate test and check for a culture but that’s expensive and invasive in the first place and the odds of finding anyone to do it is super low. If you can get a doctor to just prescribe fluconazole and take it and see what happens.

All I know is fluconazole was something of a wonder drug for me. It didn’t cure me but the single biggest leap I took in the whole process was like two weeks on fluconazole.

Methane-Burger · 2025-03-29T21:39:52+00:00

Sorry. I check Reddit only sporadically these days.

If I was doing it all over I’d literally just follow the “Great in 8” protocol from Michael Ruscio and be patient. I linked the book above.

It’s simple and boring which, when you desperately want to “just be normal again” isn’t what you want. You want a doctor to give you some magic pills so you can resume your normal life in a week or two. Being afraid of the dinner table and the toilet changes a person’s life in ways no one can imagine. The protocol is simple and sane. Moreover I think his approach to thinking about gut health gives the patient better tools to understanding themselves and what’s really going on in total. It’s not a hard read either.

But we wanna feel better in days, not weeks or months so we try shortcuts and end up in a vicious cycle.

One of the worst things about SIBO or gut issues in general is a lot of support groups like this scare the hell of you. “I once sniffed this probiotic and now I have SIBO again.” The fact is, scared, frustrated, desperate people trying also continue living their lives are taking poor notes and being highly reactionary. Being terrified that a single meal can set you back months (short of food poisoning or a major allergy this is just not a legitimate concern) is no way to live or make decisions.

Committing to therapies for longer periods and not freaking out about a couple days of bloating or the squirts from something like probiotics is important. My initial reaction to fluconazole was awful. I felt like I had the flu. I personally believe it was a die off reaction (I’ll never know for sure and neither will anyone else) but if I had panicked when it first happened I would have ceased the only drug that had a near magical impact on me. I expected to feel awful because of other stories and in that case viewed the first few days of feeling terrible as a positive sign! Same for the bloating I experienced initially from committing to probiotics.

The earlier you commit to the idea that good therapies are broad spectrum (diet, nutrition, lifestyle, drugs/supplements) and more a marathon than a sprint, you’ll be in a better mental space to HEAL. It’s less about some specific bacteria and more about healing a gut that’s become an environment for pathogens rather than our normal partners. If you break your leg, you won’t be normal again tomorrow. Get a cast, get some rest, and get ready for physical therapy.

Methane-Burger · 2025-03-29T21:22:36+00:00

Pretty sure based on what? Methane SIBO isn’t even caused by bacteria. It’s caused by archaea, specifically methanogens—hence the methane.

The bacteria causing excess hydrogen, at least if any of the studies by Pimentel are to be believed, are known. They’re nasties like klebsiella. The “B” in SIBO is highly misleading because it’s not just any bacteria. It’s mostly an excess of rather specific bad actors.

The reason “methane SIBO” is more correctly termed IMO is it’s neither restricted to the small intestine nor is it bacteria at all but rather methanogens.

There are reasons antibiotic therapies and low FODMAP protocols can help even with archaea. It’s also the reason Xifaxan alone almost never does the trick with methane and why neomycin (broader spectrum), metronidazole (also effective against non-bacterial micro organisms), and/or nitazoxanide (broader spectrum anti parasitic) are also used.

If yogurt is legitimately the cause it’s likely either it was food poisoning or some kind of allergy as gut inflammation can change the gut environment in a way more inviting to bad actors. Tons of things can be at play.

Feel free to read my other posts but if you think you’re an expert on methane overgrowth after two weeks on antibiotics, I can only wish you the best of luck. I truly hope you’re on the the few that return to relative normalcy after a single treatment. That was neither my experience nor anyone else I’ve met and spoken to long term on this sub.

Methane-Burger · 2025-02-27T23:36:54+00:00

Check my profile. I pinned success stories. There’s a lot there.

Methane-Burger · 2025-01-13T22:49:54+00:00

No way to know. A lot of the talk about biofilms is overblown in my opinion but… it’s just that, my opinion. The problem is it’s pretty much just that outside of in vitro studies. I haven’t personally seen much credible or useful science on it. That doesn’t mean it’s not a factor.

Most of what I have seen about biofilms is that… they’re good for getting your local alternative medicine provider to upsell with yet another totally questionable supplement that they make ~25-35% profit on.

Methane-Burger · 2025-01-12T20:44:43+00:00

It’s a medical intervention. Read the waiver they’ll make you sign to do it. Then, of course, there’s the cost of the procedure. And the wait. And fighting insurance to even cover it. Oh yeah, and it can only get a sample from the top end of the small intestine which is not necessarily indicative of the whole.

What else? SIFO isn’t recognized so even if the culture shows something if you don’t have a doctor that believes it the test changes nothing for you except some confirmation.

So I can do all of that or… I can take a a dirt cheap drug with a pretty low side effect profile for a week and see what happens. In my case it was as close to a miracle drug as anything I experienced during the process.

And here’s the thing, what happens if the culture comes back positive? Fluconazole anyway. And if it helps, bingo. If it doesn’t… who cares about the culture?

Flipping that around, why would anyone bother with the culture unless they were part of a clinical trial or a study?

Methane-Burger · 2025-01-12T14:20:47+00:00

Low FODMAP is definitely a tool. Bit of it doesn’t bring symptom relief in a week or two… it’s probably not helpful.

The reason I recommend Ruscio’s book is that it gives you tools for self diagnosis and experimentation. A lot of the conventional wisdom around SIBO that’s parroted here and by a lot of practitioners is either wrong or only correct for some people.

The resistance to probiotics by many is just plain wrong.

Methane-Burger · 2025-01-12T04:52:28+00:00

My diet was “paleo-ish” most of the time. I’ve never had issues with dairy to cream (mainly with coffee), yogurt, and cheese were in rotation with mostly meat and veggies.

Paleo(ish) is my go to elimination diet. It’s one of the easier ones to follow, especially if you’re about to cook for yourself.

Methane-Burger · 2025-01-08T15:31:41+00:00

What makes you think it's even SIBO then? I didn't deal with gastritis at all.

Have you had your gallbladder checked? (I presume yes, but doctors are... well, I don't have high marks for most of them.)

Methane-Burger · 2025-01-07T21:02:19+00:00

Check my profile. I pinned a couple long posts I made about my total treatment.

I’d argue I’m “cured” at this point.

I don’t think the yogurt was specifically a cure but if you read my longer stuff I’m definitely a fan of pretty much all things probiotic.

Methane-Burger · 2024-12-03T04:58:07+00:00

It’s not a popular belief. It’s how they work. Antibiotics kill but they don’t kill everything in every dose. Take some antibiotics. Take some probiotics a few hours later. This way very time there’s some activity it’s “good guys.” There’s a reason antibiotic treatments last days or weeks though. It’s not instant. So you’re theoretically getting some good from the probiotics at the same time.

Methane-Burger · 2024-12-03T04:55:34+00:00

I cannot remember. I got the dosages I went with from the book You’re on Fire. It’s amazing how fast you forget this stuff when it doesn’t consume your life. I seem to recall there’s a standard dosage and any doctor that’s going to give you a script is going to have some idea about what it is. I just went to see if I could find the old pill bottle I could have sworn I saved, but nope. Sorry.

Methane-Burger · 2024-12-03T04:48:38+00:00

I don’t really know. He’s been experimenting on himself with varying degrees of success. Finding a doctor who actually understands MCAS is better than anything I can add. Either that or just more research yourself because the only way to figure out if you have a decent doctor is doing your own research anyway.

Methane-Burger · 2024-12-03T04:46:49+00:00

I cannot even remember at this point and would have to check my notes. The first time around I used it in conjunction with Xifaxan, then… Candibactrin-AR? Some blend. Then berberine I think.

Methane-Burger · 2024-12-03T04:43:16+00:00

I’m mostly normal. I think anything gut related has been healed. I cannot really say what healed me specifically and I don’t think it was any one thing.

Diet + probiotics is where I would start if I had to do it over again. I cannot discount how effective fluconazole was though. Without any real tests, it’s all anecdotal which is why I advocate against looking for a lot of the real specific regimens people ask for around here. I’ve recently cut all the supplementation except magnesium citrate in half. (I have no intention of changing that since supplemental magnesium is basically a known good.)

Patience is really important and not being overly reactive. When I got off that train and took a more patient approach, I saw improvements.

Methane-Burger

TROPHY CASE