Confused about methane SIBO diagnosis + treatment plan
This may be long, but I am really looking for some insight from others (especially those who may have be in a similar situation).
I was recently diagnosed with SIBO and told I have methane-dominant SIBO, but looking at my test I am definitely Hydrogen dominant too plus IMO. My integrative doctor didn’t seem very confident with my treatment plan and that alone made me feel like this wasn’t a very individualized approach, ESPECIALLY in my complex case.
Here’s where I’m confused: My symptoms do NOT match what I’ve read about methane SIBO at all. I’ve had loose stools, urgency, and go to the bathroom up to 3–5 times a day for the past year or two. Definitely not constipated. Recently I started eating overnight oats, and it’s the first time in years I’m not running to the bathroom constantly. That seems… opposite of slow motility?
The protocol I was given is: Xifaxan, Neomycin, Nystatin, Digestive enzymes, Candibactin AR + BR, Low FODMAP diet (although my sheet is way more aggressive - no rice or potatoes - than actual Low FODMAP diets), cut out all current supplements I am on.
This feels super aggressive, especially all at once. I’m also really concerned about neomycin because of the black box warnings. I’ve seen a lot of people say it made them really sick too. On top of that, I have PCOS and suspected MCAS, long history of gut issues since childhood (food sensitivities, “candida,” etc.), chronic inflammation + nervous system dysregulation, recently developed random rashes that won’t go away, along with hormone imbalance since starting birth control in 2020.. I was NOT told to stop probiotics or berberine (or any of my supplements for that matter) before my SIBO test (which I’ve now read can affect results??) I’m also worried about doing an aggressive low FODMAP because of histamine issues.
Honestly, it feels like we’re jumping straight into “kill everything” without understanding the root cause. And my doctor already said I’d probably need to do the treatment twice, which doesn’t inspire confidence.
My questions:
Has anyone been diagnosed methane-dominant but had diarrhea/urgency instead of constipation?
Did anyone regret doing antibiotics vs going herbal route first?
Has anyone had false SIBO results from not stopping supplements beforehand?
If you have MCAS, PCOS, or hormone issues, did treating SIBO help or make things worse?
Would you pause and retest before starting something like this?
I’m not against treatment — I just want to make sure I’m not making things worse or missing something bigger without figuring out the true root cause.
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@thedesert
H2S was a problem for awhile, but was taken care of with the supplements. I think the emulsified Oregano OIl, eliminates the bacteria, and Flaxseed in the diet. I have bismuth on my list, but H2s is no longer an issue.
Thanks.
How are you doing now? I believe I have had SIBO-methane for over 5 years. I believe that due to the diarrhea/loose bowels and numerous movements a day that my heart has been effected. My LAD IS 75%blocked. I am 75, active, non smoker, believe in eating organic and real food.
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1 ReactionI am not sure if there is a heart connection, but I had a NSTEMI 3 years ago and had a stent placed in my LAD due to blockage. My GI PA does not want to address the methane results until I have an endoscopy with Ultrasound and Colonoscopy, which is scheduled for mid-August. I have been trying some home remedy things - chia seeds mixed into applesauce, letting is sit a bit and eating it. I have not noticed much of a change. I also am getting some episodes of gastritis which nothing seems to help. The episodes start around 2-3 AM and last about 24 hours or more. Not sure if that is related to the excess methane or not. Thanks for asking how I am doing. I hope you can get relief.
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1 Reaction@hallward I have never heard of a calprotectin test. I definitely am going to look into it.
I'm ignorant about these acronym alphabet diagnoses, but the orig. story made me recall a close friend who had a frightening bout of diarrhea, causing weight loss and much stress. She had myriad tests and diagnoses but didn't tell her Docs all the supplements she was taking daily. She disclosed SOME of them, but not all. Finally a very stern Doc demanded to know the full list and discovered that she was taking too much magnesium!!! So simple! (I note the reference to berberine in the OG; which can cause diarhhea.) Supplements can upset balances and cause lots of problems. Just sayin'.
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1 ReactionThanks for the input. I take 100 mg of magnesium glycinate every night. I have tried a trial of stopping it for a month - no difference in my patterns. As someone who has multiple cardiac conditions, I also have to keep my magnesium within acceptable levels. Besides that nightly pill, I only take CO-Q10 as another supplement, no others.
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1 ReactionWow - let me tell you my story (quick version). I had SIBO (C) for a few years and chased the problem with Xifraxan/Neomycin about 6 times. Seems to help but I finally figured out that the SIBO was really a symptom, not the problem. So I started on a diet (FODMAP) while I took antimicrobials to fight the Archaea in my small intestine (same effort as the antibiotics), but I also took some for gut health, and some for my motility. I then come to understand the timing issue (Migrating Motor Complex - MMC). Get the right environment for the body and it will work to correct many conditions. In my case, my eating habits were not good compounded by being low on certain enzymes (found out much later). A few basic things got me over the SIBO (c) or IMO.
1- Drink plenty of plain water ( I did 64 oz/day).
2- Three meals per day with no snacking ( nothing with calories in between meals). 4-5 hours between meals and dinner to breakfast - 12 hours.
3- Chew my food well, don’t be in a hurry.
4-FODMAP while treating the problem (not a long term plan). Still want to keep a balance of protein, carbs, minimize added sugar, fats etc. Basic health eating. I ate salmon twice per week, sardines in olive oil twice per week, lean beef twice per week and a lot of chicken.
5-I took antimicrobials (Atrantil, emulsified oregano oil, Allicin, and Berberine. (Antibiotics probably would have worked for this part). (I think antacids probably helped create my problem - be careful with those- your body need stomach acid in the right amount).
6-Sunfiber, Ginger, and artichoke,/ginger, zinc/Carnosine, L-Glutamine, Tumeric and CoQ-10. Suggest you investigate these and see what makes if any for you possibly.
Eventually I cut back on what I was taking (took me about 10 weeks).
7- Work with a good dietitian (versed in SIBO, not just any dietitian), as well as your doctor.
8- Read the book: The Microbiome Connection: Your Guide to IBS, SIBO, and Low-Fermentation Eating
by Dr. Mark Pimentel (Author), Dr. Ali Rezaie (Author) .
Hope you are as lucky as I, and get past your SIBO problem.
Note: I also used some Chatbots to help correlate data quickly. Big help. Correlate between 2 chatbots, sometimes they don’t agree.
I too was diagnosed with SIBO and methane gas issues. I took the same prescription drugs that you did. They did work for a very short period of time. However everything went back to bloating after I eat. I never had constipation. I did have diarrhea though and now I’m at a loss. I did the fob map Diet and still had gut issues. I am trying to do gluten-free now and dairy free and see what happens. But I cannot lose this XX weight that I’ve gained.
I have had SIBO for 10 years. I have methane but with it diarrhea with at least bms 3x a day. Diagnosed last year after extensive testing. I am 74, always been active, lifted weights, eating healthy mostly organic food and maintained a healthy weight. Last year my LAD was 50%+ blocked. This year, cardiologist says LAD is 75% blocked. I also had bone scan and I have osteopenia. In my opinion SIBO is/has been detrimental to my overall health. Online it indicates that it is the inflammation that causes the health issues. What else are people doing to decrease inflammation.
Lots of good questions here but I can only respond to one. My history: NET, small intestine surgery '22, skin cancer (chemo then treatment) '23, Colon cancer and discovery of more NET-- '24 (removal, necrosis of colon=surgery 2 w/ ileostomy, resection '25. I have had digestive issues since 11/24. I am now lactose intolerant. My body weight was way low, yet I followed all post surgeries diet recommendations; FODMAP, BRAT, modified BRAT, etc. Was taking immodium to try to slow things down. Nada. Bottom line: It has been a year of what you are describing. Yet the NP insisted that I had overflow diarrhea and went through 3 times the recommendation to clean me out. Nov '25--discovered Bile Acid Malabsorption. Started Cholestyramine, not much effect. April '26 Finally did a motility study that my body failed as the nuclear meds were completely thru my system in less than 24 hours. Moved on to SIBO testing--positive for BOTH kinds (remember that diarrhea is my issue also and my body is not processing foods, therefore mineral and vitamin loss). Two rounds of different antibiotics---no good body response. Currently exploring (via Dr. Miller--good AZ Mayo doc!) Bile Acid Diarrhea.
Have you done full panels of GI testing? What have you ruled out? I have an expanded diet now of eating things with fiber and am making incremental improvement. It gives me hope and I've gain some weight. Gas solution? Iberogast working better than GasX. I carry a backpack of emergency supplies for blowouts, complete with a change of clothes. Persistence will pay off!
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