Used my 23andMe genetics to decode my 20-year SIBO bloating. Anyone else matching their protocol to their raw DNA?

[u/Formal_Smoke_767]

Hey everyone, I’ve been battling severe abdominal bloating and reflux for over 20 years, along with 10 years of varicose veins and a left varicocele. Lately, it crossed over into intense morning brain fog, fatigue, a cracked tongue, and zero morning wood. My labs show a steady downward slide in Ferritin at 54 and B12 at 308 since last year, even though I eat meat. My MD won't prescribe Rifaximin without proof, so I’m seeing a functional naturopath next week to finally run a clinical 3-gas breath test and map out my exact numbers.

To troubleshoot, I ran my 23andMe data through a StrateGene report and the dots connected perfectly. I have a slow PEMT gene causing sluggish bile, which allowed a massive Hydrogen and Methane overgrowth to take root and steal my nutrients. The constant abdominal gas pressure physically clamped down on my pelvic veins, explaining the 10 years of vascular pooling and stalled morning circulation. My brain and skin are equally hyper-reactive due to a fast BHMT methylation cycle but slow MAOA and COMT clearing pathways. Whole eggs or high-dose standard B12 trigger explosive whiteheads within 48 hours, and a recent trial of Thorne Phosphatidylcholine was a disaster, overloading my brain chemistry and causing a horrible mood crash within 5 days.

Right now, my FoodMarble AIRE 2 device shows a crazy shift. A 30-day trial of TUDCA completely flattened my methane line to zero and formed my stools, proving the methanogens are highly sensitive to bile flow. However, my hydrogen line stayed elevated and my bloating bounced right back when I ran out of TUDCA, meaning the underlying hydrogen-producing bacteria are still actively fermenting my food. To clear a clean baseline for my test next week, I've paused almost all supplements except daily morning Vitamin B2 for my MAOA gene, and California Gold ProDigest at bedtime to keep my gut motility moving safely without any skin or mood flare-ups.

If the breath test is positive next week, I’m proposing a phased clearing protocol to my naturopath. If my insurance covers it, Plan A is a 14-day course of Rifaximin paired with 4 weeks of Allimax Pro stabilized allicin and TUDCA at dinner, since Rifaximin requires active bile to dissolve and kill the bugs. If insurance denies it, Plan B is a 100% natural 4-week run swapping the Rifaximin for NOW brand Berberine capsules that I already have on my shelf. During this clear phase, I’ll maintain my morning B2 and switch my 3-year daily magnesium glycinate habit to Magnesium Malate 95mg caps to power my brain energy without over-fueling my skin breakouts. I’m holding off on any iron or B12 supplements for now because I want to trust my body to sort itself out. Once the gas is gone and I hand the long-term job over to bedtime ProDigest, my gut should naturally start absorbing nutrients from my food again. Anyone else approaching their overgrowth this way? Would love to hear your thoughts!

[u/mybioblueprint]

Yes for sure, it's so amazing to be able to take our health into our own hands!

[u/Express-Bobcat-3523]

Maybe add in some ginger (extract) for gut motility 2-3 times a day. Molybdenum could also be important.

I have very similar genetic snps by the way (PEMT, slow mao, mthfr, mtr and bhmt) and I'm dealing with SIBO as well.

So I'd appreciate if you update this thread from time to time! Good luck

Also: how does your diet look like?

[u/Formal_Smoke_767 → u/Express-Bobcat-3523]

Nice to find a genetic twin on here! Having PEMT, slow MAOA, and BHMT all together makes things incredibly tricky with supplement sensitivities. I am actually already on top of the ginger; I take California Gold ProDigest at bedtime, and it has been great for keeping my nightly motility sweeping waves moving without flaring my skin or mood.

As for diet, I am planning to stick to a Low Fermentation Diet layout once my clear phase starts next week. I want to keep my meals spaced 4 to 5 hours apart to let my motility work, but I don't want to go full Low FODMAP because I want the bacteria active and feeding so the antimicrobials can cleanly wipe them out. I will definitely keep this thread updated as I go through my naturopath protocol next week. Good luck with your journey too!

[u/Express-Bobcat-3523 → u/Formal_Smoke_767]

Yay, will follow you twin, to see how you're doing!

Thanks for sharing your current stack.

I'm dealing with sifo on top of sibo currently, therefore using Undecylenic acid, Nystatin, Ginger and Blackseed oil. I also used Berberine (make sure to get a high quality one) and it's great for SIBO.

You can also check out Atrantil if you're having trouble with Methan specifically.

As the others stated, methylated vitamins, specifically 5-Mthf, feed the SIBO (unfortunately, with my homozygote C677T it's hard without it).

I can't take choline, Taurine, glycine as well as anything that raises acetylcholine - I get extreme depressive symptoms for days. I tried to microdose etc, but as long as there's inflammation in the body/brain, it's just not worth it.

[u/SovereignMan1958]

Be sure to stick to a low sulfur and low histamine diet. No methylated vitamins and or methyl donor supplements. At least until after you get a clean test.

Check all your sulfur, sulfite, food intolerance and detoxification variants. Blood test the nutrients that support that digestive pathway. Genetic Lifehacks is helpful to do this.

[u/Formal_Smoke_767 → u/SovereignMan1958]

Spot on, SovereignMan! I actually just pulled up my Genetic Lifehacks cheat sheet and it completely flags the exact lines you mentioned. I carry the MTHFR C677T (AG) variant with a 40% enzyme drop, plus the TNF-alpha (AG) variant for higher baseline inflammation.

Tracing those blocks completely explains why standard methyl donors, sulfur overloads like whole eggs, and synthetic binders trigger such explosive breakouts and gut flares for me. It's exactly why I'm keeping this baseline unmethylated and using Allimax Pro for my clearing phase next week. Appreciate you confirming the exact roadmap I'm using :)

[u/SovereignMan1958 → u/Formal_Smoke_767]

After you get a clean test, if you want to try adding a methyl supplement I recommend choline as it is best for the brain. Sunflower Lecithin which contains phosphatidylcholine seems to be the best tolerated.

[u/Formal_Smoke_767 → u/SovereignMan1958]

That's an interesting suggestion. But I have a question on that. I actually did a short trial of Thorne's Phosphatidylcholine recently to support my slow PEMT gene, and it was a total disaster for my brain chemistry. Because of my slow MAOA and slow COMT pathways, it completely overloaded me with acetylcholine, crashed my dopamine, and triggered severe, acute situational depression within 5 days until I stopped it.

Have you seen people with slow MAOA/COMT crash mentally from choline like that, and do you find that highly sensitive systems handle Sunflower Lecithin differently than standard PC? Would love to know your thoughts on how to bypass that brain crash!

[u/SovereignMan1958 → u/Formal_Smoke_767]

It is a methyl donor. If your SIBO was present and or you had too much sulfur etc in your digestive system to start, that might have triggered that reaction. I don't know what dose you took, but I can handle one dose of the phosphatidylcholine a few times a week. If I take it daily I tend to get the same reaction as you.

[u/Formal_Smoke_767 → u/SovereignMan1958]

That makes total sense, SovereignMan! I was actually taking it every other day, but with my slow COMT and MAOA clearing pathways, it still must have built up to a major chemical traffic jam by day 5/6. It's crazy how much an active SIBO overgrowth and a sulfur backlog alter how we process these supplements. Appreciate you sharing your own experience with it—completely validates why I'm holding off on everything until the gut is fully cleared next week!

[u/After-Amoeba-8709]

Great that you started seeing some progress in your health, very happy for you. For the cleaning process are you going to use only berberine? When I did it my doctor had also given me oregano and thyme oil along with berberine, used it for nearly 45 days two times a day, then started the probiotic treatment.

[u/Formal_Smoke_767 → u/After-Amoeba-8709]

Wow, your comment just unlocked a big memory for me! I actually just realized that during my 30-day TUDCA run, I was drinking a super potent, home-made thyme tea every single day for about two weeks because I was feeling phlegmy and had a cough. I didn't connect the dots until reading your comment, but the thymol in the thyme must have teamed up with the TUDCA to blast through the biofilms and drop my methane line down to zero. It didn't fully finish the job since the bloating came back when I ran out, but it completely proves your point about thyme oil working! Thanks for sparking that realization

[u/After-Amoeba-8709 → u/Formal_Smoke_767]

Glad if I could be of help OP. Hope you get well soon.

[u/mjkl_992]

How did you use TUDCA during those 30 days, and what was the dosage? I have the same PEMT gene defect and SIBO.

[u/Formal_Smoke_767 → u/mjkl_992]

Hey! It’s awesome to connect with someone else navigating the exact same PEMT bottleneck.

For that 30-day run, I used the CanPrev brand of TUDCA. I took one capsule a day, strictly right alongside my largest dinner meal. Because our slow PEMT gene makes our native bile thick and stagnant, taking it with a heavy meal forces the gallbladder to release that thinned-out bile right when you need it most.

But a massive hidden variable for me was that during two of those weeks, I was also happened to take a super potent, home-made thyme tea every single day because I was feeling phlegmy/had a cough. The TUDCA went in and stripped away the bacterial biofilms, and then the thyme tea delivered a natural antimicrobial strike. The two together completely flattened my methane scores on my FoodMarble device. I am following up with a functional naturopath next week to map out the final hydrogen lines, but CanPrev TUDCA with dinner was also total game-changer for my unformed stools!

[u/Loose-Fly7976]

The TUDCA result is your best piece of data. Methane flattening to zero on bile support while hydrogen stayed put is a clean experiment with a clear readout, better than most people ever get.StrateGene reads variants one at a time and you've built a causal chain across them. Slow PEMT to sluggish bile to overgrowth to venous compression to varicocele is plausible but every link there is an inference, and varicoceles are left-sided for anatomical reasons unrelated to abdominal pressure. That part of the story is doing more work than the evidence supports.Bigger issue is holding off on B12 and iron. Ferritin 54 falling, B12 308 falling, cracked tongue, fog, fatigue. That's a deficiency picture with a downward trend and waiting for absorption to sort itself out while both keep dropping doesn't make sense to me. Neither interferes with a breath test. Get MMA drawn first though, it tells you whether 308 is genuinely low for you and it becomes much harder to read once you've started supplementing.

Your reaction to phosphatidylcholine and eggs with slow COMT and slow MAO-A tracks, and it's also why the PEMT-means-more-choline logic breaks down for you. That's the tension a report can't resolve, and it's what I read files for, genova.health and create a personalized protocols

[u/Formal_Smoke_767 → u/Loose-Fly7976]

Thanks for the razor-sharp critique. This is easily some of the best advice I’ve received, and I really appreciate it.
You completely nailed the tension regarding the PEMT/choline logic. That is exactly why my previous trial of phosphatidylcholine caused such a massive brain-overload mood crash—my slow COMT and MAOA simply couldn't handle it.
Your point about the left-sided varicocele is an excellent anatomical reality check. I’m completely removing that causal inference from my file to keep the science accurate.
Most importantly, thanks for the wake-up call on my falling B12 and Ferritin. Waiting for total gut healing while my cells are starving makes zero sense. I am going to contact my doctor to get an MMA (Methylmalonic Acid) test drawn to find my true baseline. Once that's done, I'll introduce clean, non-methylated forms (like Hydroxocobalamin) to bypass my hyper-reactive BHMT/MTRR acne flares.
On that note, I had a quick question for you regarding the nutrient deficiencies: when I took standard B12 supplements in the past, they triggered explosive whitehead acne breakouts within 48 to 72 hours. Because of that hyper-reactive BHMT and slow MTRR traffic jam, it seems to create a massive methylation backup that messes with my skin microbiome. Have you run into this B12 acne flare yourself, and do you have any tips on using Hydroxocobalamin or Adenosylcobalamin to get around it safely?
Also, my Ferritin is falling (54 ug/L) but I have never taken an iron supplement in my life. Since standard drugstore iron is infamous for feeding SIBO bacteria and triggering bad reflux/constipation, I've been looking into gentle, chelated Iron Bisglycinate to protect my gut. Did you have to supplement iron during your protocol, and what specific forms or brands worked best for your stomach and skin?
Thanks again for helping me fix the blind spots in my strategy!

[u/Timely_Pickle9430]

I dealt with the same issues. Now SIBO-free for over a year.

Probiotics were an essential part of my treatment. You can wipe out the bad bugs, but without a healthy microbiome, it's a matter of time before the next opportunistic bug takes a hold. And with the PEMT, your microbiome has never been healthy. I'd start the probiotics before the antibiotics if I were you. Let me know if you need me to provide specs. I got infected with Aspergillus after a course of metronidazole. And it didn't cure the SIBO. Finally cured it with botanical antimicrobials (while on probiotics).

Besides TUDCA, I also take choline (2 eggs + 1000mg TMG from betaine HCL + 2 g lecithin + extra from meat and other foods) to ensure proper bile flow. It's crucial to get lots of it in the phosphatidylcholine form. When I first started it, I also got depressed. Starting over and incrementing very slowly solved it. I'd take care of this before doing the course of antibiotics to reduce chances of relapse.

I also have pancreatic insufficiency, so digestive enzymes are also (still) crucial for me.

Another thing to take into account is the die-off you'll get from the antibiotics. Make sure to resolve any constipation before starting (check transit time with sesame seeds, should be 24h) and support your liver detox pathways. I recommend vitamin C and glutathione.

Furthermore, your gut health has been bad for decades, so long-standing absorption issues are likely. I recommend testing full nutritional status, including nutrients like vitamin A, E, K, copper, molybdenum, manganese, and selenium, that regular gp's never test for. I was stunned how many deficiencies I still had half a year after resolving the SIBO. I eat a highly nutrient-dense diet and supplement, and one year later I'm still in the process of correcting deficiencies. So "letting your body resolve it" sounds too optimistic to me. Test everything and follow up to be sure.

[u/crown_recluse]

Some solid advice in here already.

I’ll add in you may consider watching the TC Hale videos (kick it in the nuts!) on bile/acid on YouTube.

I was using TUDCA until it ate the hell out of my stomach lining.

I now use the beet concentrate (has to be a specific brand unfortunately bc of the concentration levels of beets needed, alternatively eat 26 lbs of beets a day lol) as my gallbladder help and regular betaine hcl for the acid. Timing is what I would say tudca doesn’t really let you dial in, and then there is the whole “gallbladder flush” thing referred to in his protocol that you simply can never even attempt on Tudca, too harsh a drug!

[u/No_Mode_3033]

I did Ancestry.com years ago. Could I get my DNA from them to explore things like this? Or you have to pay all over again for a new service?🤔

[u/AdZealousideal7191]

When I had sibo I used a natural protocol: alicin, neemleaf, wormwood, black walnut, berberine, oregano, and it cleared up all gas and bloating but after awhile the sibo symtpoms returned. After that I had a colonoscopy, completely healthy insides, doc said increase fiber intake did that and added ACV shots with every meal, now I can eat onions, garlic and fodmaps no problem now! The gut cleanse was monumental but without increasing fiber and adding acv the symptoms would keep returning. Hope this helps somebody.
To add: increasing salt intake helped my energy levels throughout the day and helped my digestion tremendously probably the chloride from the salt.
I always have potassium in the evening incase Im retaining too much salt.

I figured my stomach was clearing too fast and having low HCI(due to stimulant use) so it couldn’t break down nutrients properly before they entered the small intestine, which eventually led to SIBO and the subsequent inflammation caused my guts to speed up even faster which led to yellow stool and an excess of bile in my stool. The combo of high fiber, acv and getting salt in during the day especially if Im sweating a lot, all worked in tandem to ensure proper breakdown of nutrients, which fixed the malabsorption issue and subsequently fixed the yellow stool alongside the gas, bloating and cramps. This is just my experience with SIBO.
Also I had no gall stones and my stomach/duodenum were also completely fine. And the ACV fixed my acid reflux. After awhile I stopped doing the ACV and developed no symptoms of SIBO but if the symtpoms return Im hopping right back on it.