Confused about methane SIBO diagnosis + treatment plan

Posted by jontae @jontae, Apr 3 12:45pm

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.

Interested in more discussions like this? Go to the Digestive Health Support Group.

Profile picture for lucyvt @lucyvt

@jlharsh Thanks for your kind words. It has been a lot of 'stuff' for sure. My hip is great. I had my left one replaced 2 years ago and it is great too - no complications after it so I was totally unprepared for this mess. Having to be resuscitated is very unnerving. I knew I was in afib as I had one isolated episode of it before. The nurse in recovery was ignoring me when I was telling her that I was in afib. Finally, my heartrate climbed high enough that she had to get a dr in to help. Anyway, the GI stuff has been going on a while. I have a lot of discomfort and especially in my right upper quadrant. Lots of loose stools. No constipation. My PCP referred me to gastro earlier this year and the SIBO test was the first one that was ordered. The hydrogen was 2 and never rose. The lactulose they gave me for the test caused horrible diarrhea when I was on my 2-hour ride home in rural Vermont, with only one rest stop available! That was fun. I also have rheumatoid arthritis and am a 2-time cancer survivor, so I am good about advocating for myself and asking lots of questions. My gallbladder was full of stones and there were lots of adhesions everywhere. Not sure if anything is related to my other health issues or not. Oh - I almost forgot - i have heart failure also. I am seeing a PA-C in gastro and wonder if my complications/comorbidities might be too much for her. She is great but I really want some answers.

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Hmmmm, @lucyvt you have so, so much going on. I do have a couple thoughts.

You may want to go to the Connect home page and see what you can find using the search feature. I want to do this as well but it may take me some time. I will let you know if I find anything.

You must take medications and they may come into play. Your conditions may not all be isolated things going on.

Have you considered going to an academic medical center, or one that takes an integrative approach to your various treatments, perhaps finding a possible root of what is going on?

You can certainly pursue an appointment at Mayo Clinic either with one of your doctors referring you, or pursuing yourself. Use this link: http://mayocl.in/1mtmR63

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Profile picture for lucyvt @lucyvt

@jlharsh Thanks for your kind words. It has been a lot of 'stuff' for sure. My hip is great. I had my left one replaced 2 years ago and it is great too - no complications after it so I was totally unprepared for this mess. Having to be resuscitated is very unnerving. I knew I was in afib as I had one isolated episode of it before. The nurse in recovery was ignoring me when I was telling her that I was in afib. Finally, my heartrate climbed high enough that she had to get a dr in to help. Anyway, the GI stuff has been going on a while. I have a lot of discomfort and especially in my right upper quadrant. Lots of loose stools. No constipation. My PCP referred me to gastro earlier this year and the SIBO test was the first one that was ordered. The hydrogen was 2 and never rose. The lactulose they gave me for the test caused horrible diarrhea when I was on my 2-hour ride home in rural Vermont, with only one rest stop available! That was fun. I also have rheumatoid arthritis and am a 2-time cancer survivor, so I am good about advocating for myself and asking lots of questions. My gallbladder was full of stones and there were lots of adhesions everywhere. Not sure if anything is related to my other health issues or not. Oh - I almost forgot - i have heart failure also. I am seeing a PA-C in gastro and wonder if my complications/comorbidities might be too much for her. She is great but I really want some answers.

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@lucyvt @jlharsh I forgot to say my methane was 53 ppm at baseline and rose to 79. So it was high at baseline already during the SIBO test.

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Profile picture for Janell, Volunteer Mentor @jlharsh

Hmmmm, @lucyvt you have so, so much going on. I do have a couple thoughts.

You may want to go to the Connect home page and see what you can find using the search feature. I want to do this as well but it may take me some time. I will let you know if I find anything.

You must take medications and they may come into play. Your conditions may not all be isolated things going on.

Have you considered going to an academic medical center, or one that takes an integrative approach to your various treatments, perhaps finding a possible root of what is going on?

You can certainly pursue an appointment at Mayo Clinic either with one of your doctors referring you, or pursuing yourself. Use this link: http://mayocl.in/1mtmR63

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@jlharsh My Gastroenterologist is at Dartmouth, as are my 2 new cardiologists - one for the HFpEF (heart failure) and the other for the Afib. My rheumatologist is independent and she is really the most integrative of all of my doctors. My pulmonologist, PCP and endocrinologist are at University of Vermont. I forgot I have osteoporosis and adrenal insufficiency. Both Dartmouth and UVM are teaching hospitals. Thanks for the thought about Mayo Clinic. I will think about it. I do not travel much as I have a medically involved dog, and it is hard to find care for him.

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Profile picture for beebe @beebe

Be kind to yourself and skip the Xifaxan, Neomycin, and Nystatin for now. They are only treating a symptom and not a cure. I did herbal treatments two times and the effect lasted for 1 week each time.
That set me on the path to trying the low FODMAP diet and carbohydrate restriction. Look up Dr. Norm Robillard's Fast Track Diet, it restricts carbs that ferment readily like pasta, rice flour, juices, some fruit, and of course cakes/cookies.
https://digestivehealthinstitute.org/fast-tract-diet/
The fast track diet uses a point system to rate foods and portions of those foods, sometimes you can eat a highly fermentable food if you keep the portion small. There is a really low cost app for both the Monash university FODMAP diet as well as the Fast Track diet which I find really helpful.

If you do the work you will discover what is causing your digestive issues. After completing the FODMAP elimination diet I found I was sensitive to fructose and fructans at amounts that should be safe under the FODMAP diet, honey is a big no-no for me. When I get a hint of acid reflux (the first sign of SIBO for me) I cut back on carbs and try to figure out what food I ate too much of in the past 3 days.
Hopefully when you find the foods that are upsetting your digestion your rashes will go away. I had a knee rash since early childhood which went away when I gave up gluten. If you have a tendency towards psoriasis peppers and potatoes can cause a rash. This may sound stupid, but if you have sensitive skin be careful with how much laundry detergent you use and skip the fabric softeners. I was getting a rash and it was from my laundry detergent so I cut the amount I use and it went away.
Link to Norm Robillard and histamines on YouTube


You can schedule a phone appointment with Dr Robillard and talk through your issues. I had tried the Fast Track diet and kept my fermentation low in the low 20's for over a week. My symptoms should have resolved, he told me "Something else is going on". He was right, I did the FODMAP elimination diet and found the fructose/fructan sensitivity issue.

Hope something I shared helps!

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@beebe yes i have to use the white bottle tide scent free one bc i have terrible eczema if i use any other

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Well - a lot for sure. My story shortened. Couple years ago it began with terrible gas and constipation/diarrhea cycle. Found that I has pancreatic insufficiency so started taking CREON. Symtptons continued. Breathe test showed high methane and low hydrogen. Started with Rifaxin & Neomycin. Two treatments and seemed good, for about 6 months and then the same again. Did this a couple times - back to gas and constipation. Did a lot of reading and research. My opinion (not a doctor) is that my problem was not the Archaea in my small intestine ( that is a symptom, not the problem), but that my digestive system is out of whack. More research and found that anti-microbials can work against the Archaea (Emulsified Oregano OIl, Atrantil, Berbedine, Allicin, NEEM, MCT Oil and a few more). But I also found that my motility was also an issue, so other supplements. Then I found through research that the gut gets irritated and thus supplements to help the gut health.
Then I found about the Migrating Motor Complex (MMC). When I eat in between meals, it messes with the MMC timing, which leads to incorrect digestion. We a get away with a-lot of things when we’re young and the body has excess capacity, but when it goes off of perfect (mine is low on digestive enzymes) then digestion is more difficult. Then I realized that my problem had to do with timing of eating, what I’m eating and supplements.
Abbreviated results: This is what I did and in 4 months, my gas is gone and daily BM without stress or difficulty (you may be different but this helped me).
1- 64 oz of water per day, Body needs it work correctly.
2- Three meals per day (5 hours apart) with no snacking (anything with calories - soda, coffee etc). Snacks stops the digestive process temporarily and get the digestive capacity out of whack.
3- Low FODMAP as much as possible but try to keep it balanced.
4- Anti-microbials to kill off the archaea in the small intestine (it shouldn’t be there).
5- Gut health ; Ginger, L-Glutamine, Iberogast, Artichoke/Ginger, Tributyrin, Tumeric/Curcumin, Coc-Q-10 and Zinc-Carnosine.
6- Motility help: Miralax and Sunfiber prebiotic, but be careful of anything with inulin (possibly problematic).
7- I had low B-12 and Iron due to the archaea (showed in my blood test) so I took liquid B12 and iron.
8- These helped a great deal but wasn’t perfect. I then had an Endoscopy and it turned out that I have multiple enzymes that are low ( not zero) but lactase and sucrase were both low enough that I need supplements to help. After learning about and taking a couple of low priced enzyme supplements, I have stopped all other pills (other than CREON) and life is good.
The digestive system is slow and it is difficult to correlate what we eat vs the results. A bit of patience is going to be required.
Now, my diet is :
Sardines a couple times per week, eggs, salmon a couple times per week, lean beef twice per week and mostly chicken other than those items. This gives me good Omega 3 and other beneficial amino acids, good protein. (Note: some sources of Omega 3 are not the best, it can be confusing). Stay with the 64 oz of water, 3 meals, and a diversified diet. I take an occasional probiotic, but not every day. I’m still working to see what works for me, so I’m diversifying my diet slowly. So far - so good.
Talk to your doctor / dietitian about these and see if any of them make sense for you. Hopefully you can get your body back in sync and happy again. One last note: some of the chatbots are good research tools to quickly give you an easy way to correlate opinions and data. I use a couple of chatbots to see if they agree. Good luck.

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From my experience with SIBO, I was not given any meds that treat symptoms. It’s important to treat the cause. Antibiotics are not helpful for SIBO and actually can be a reason you have SIBO. It’s important to increase good bacteria in the gut. I was put on prebiotics and probiotics to build the good back up. I was also helped to change my diet and went dairy free, gluten free (gluten is not good for the digestive tract), and sugar free. Bad bacteria feed on sugar. I substituted stevia to get off sugar to add sweetness to my coffee or tea. I went off dairy products from cows but could eat dairy from sheep and goats milk. There are plenty of gluten breads, pastas and other items. Pasta from Italy is good as Europe grows a completely different wheat. And one bread that’s also ok is sourdough because it’s been fermented. Other fermented products that help the gut are Kefir, kombucha and Greek yogurt. A good nutritionist can help you.

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