Dietary treatment for SIBO (low-FODMAP isn’t enough~)

MatthewMysterious debilitating undiagnosable nausea.

That keeps getting worse.

Despite more than 16 months on the Autoimmune Protocol (AIP). That’s what was happening to Matthew. Even though 15 of those months were low-FODMAP.

The AIP is working~

All of Matthew’s autoimmune symptoms are reversing on the AIP.

But the nausea has not been responding. It’s been worsening. Slowly. For a year.

Until this April when he was hardly eating & was almost completely incapacitated.

We determined the nausea is NOT autoimmune & will require a different treatment. So we set out to hack that.

All the specialists, including his functional medicine doctor, have poked, prodded, tested and hypothesized & come up with nothing. Then shrugged & left us alone with a deteriorating, undiagnosed, unresponsive health issue that has caused Matthew to be unable to work since December 2013.

We’ve suspected Small Intestinal Bacterial Overgrowth (SIBO) for a long time.

Despite the fact that Matthew’s Gastroenterologist says SIBO doesn’t exist.

Small Intestinal Bacterial Overgrowth (SIBO)

SIBO is a condition in which beneficial bacteria become displaced in the digestive tract.

They migrate from the colon, where they are supposed to be, into the small intestine. This results in fermentation of carbohydrates in a part of the gut where fermentation is not supposed to occur, causing gas, abdominal pain, constipation or diarrhea, heartburn &/or nausea. Symptoms range from mild to debilitating.

SIBO causes primary symptoms, but it also contributes to intestinal permeability (‘leaky gut’) which is implicated in autoimmune & other chronic health conditions.


Treatment options include specific pharmaceutical antibiotics (such as Rifaximin), herbal antibiotics or a dietary protocol that makes a low-FODMAP AIP look like a cakewalk (at least at first).

Experts seem to disagree about whether it is possible to treat SIBO through diet alone.

Registered dietician in her book Digestive Health with Real Food, indicates that diet is a viable options for treatment of SIBO. Angie Alt of Autoimmune Paleo suggests that SIBO cannot be treated with diet alone. She references Dr. Alison Siebecker’s research to support this view.

As SIBO experts Allison Siebecker & Steven Sandberg-Lewis explain, “diet alone has proven successful for infants and children, but for adults one or more of the other three treatment options are often needed to reduce bacteria quickly, particularly in cases in which diet needs to be very restricted to obtain symptomatic relief.

After combing thorough the research it remains unclear to me whether it is truly impossible to cure SIBO through diet, or if maintaining the required protocol for a sufficient length of time is considered too difficult, or too risky from a nutritional standpoint.

We have learned that Matthew’s diet definitely needs to be very restricted to obtain symptomatic relief, but nevertheless he is taking a dietary approach.

Partly because he tried to get a prescription for antibiotics to treat SIBO but was turned down by two different doctors, who cited their own ignorance about SIBO & the fact that he was in such rough shape. Neither was wiling to risk making him worse.

According to Angie Alt, it can be extremely challenging to get a prescription for antibiotics to treat SIBO here in Canada.

So, as of a month ago, Matthew is following the elimination diet outlined by in Digestive Health with Real Food. Lots of bone broth (no surprise there!), no caffeine & the only carbohydrates he is eating currently are carrots & spinach.

This is meant to be a short-term elimination diet, until symptoms have been ‘mostly absent’ for at least five consecutive days. According to

We were pretty confident that Matthew’s gut was the intransigent type, so from the beginning we figured he’d give it an 8 week trial.

He is now 5 weeks in.

At the beginning he was almost completely disabled. Unable to care for himself.

Not only was he suffering excessively, I was drowning in stress. We were back where we’d been at the worst of his autoimmune crisis: I was caring for him; keeping the household running, including all the food prep & cooking that is required on the AIP; keeping up with a demanding career (currently our only option for income); parenting; and worrying constantly about our future.

That was our baseline.

The Results

Within 9 days on this new protocol his nausea had reduced from a 7-10 (on a scale of 0-10, in which ‘0’ is no nausea and ’10’ is completely incapacitated) to a 4-6.

Petra & Matthew 2 croppedOne month in, he is still in the 4-6 range. And as he says, the difference between  a 4 and a 6 is “at 6, I’m just tending to my immediate needs whereas when I’m a 4, I can be more thoughtful and proactive about life. Over 6 and I can’t really take care of much”.

As Matthew’s spouse, I can vouch for that.

This post is part 1 of a 2-part series. Find part 2 here.

Biohacking Autoimmune~

This Monday (May 25th) is the last chance to buy the Autoimmune Protocol Wellness bundle (& get my new e-book Biohacking Autoimmune DIY~).

Click here to view more details


37 thoughts on “Dietary treatment for SIBO (low-FODMAP isn’t enough~)

  1. I would definitely suggest acupuncture and CHinese Medicine (with a custom made herbal prescription rather than relying upon the standard herbal formulas available in pill format). A licensed or certified acupuncturist who has successfully passed the NCCAOM board exams in acupuncture and herbology is what you’re looking for; anyone else will have insufficient education to bring a holistic strategy to his treatment.

    • Thank you, Isabeau, I appreciate you brainstorming with us. Matthew has tried acupuncture (rather extensively) and spent several years with a good Traditional Chinese Medicine Doctor. We have been experimenting for a long time & are committed to a dietary approach at this point because that is where he sees results.

  2. Petra,
    Thank you for your consistent honesty. You and your family have been a beacon of hope for my family as we struggle with similar battles of autoimmune (me) and SIBO (husband, child). It’s been discouraging to continue trying one diet after the next and feel like it’s a guessing game, all the while monitoring everyone’s health responses and food reactions and or intolerances. Our next step is the SIBO clinic in Portland, OR. Have you checked them out? They offer Skype sessions with Dr. Siebeck. Keep up the great work and thanks again.

  3. I am working with my functional medicine doctor to eliminate SIBO. Had two breath tests confirming. Can you get the breath test in Canada? Best reference on how to treat…John Herron’s Gut Health Protocol. On Amazon and there is a great FB community for SIBO. Getting ready to try the prescription after months of Berberine and A.D.P (oregano oil) didn’t eliminate it. There are other herbal protocols that may help (Allicin, Neem, Interfase plus to eliminate biofilm.). I’d be happy to share off line with you my struggles.

    I bought the AIP Bundle. Wow! Such a lot of info. Thanks for compiling it for all of us.


  4. Goldenseal root is a natural antibiotic. (As with most herbs, however, you need to take a lot, frequently. Tea, anyone?) Colloidal silver is touted as a general antibiotic, too, but oh, the controversy! (Stupid people making it wrong and then taking way more than they ought to results in silver-bluish skin. /facepalm) There are alternatives. This is one bacterial case, however, where the usual “use probiotics to fix everything” is probably not going to work for you.

    I’ve got a friend who has the same problem with the nausea. I think I’ll experiment on him. Muahahahahahaha…

    • Goldenseal is actually one of the primary herbal antibiotics used to treat SIBO~. And yes, I agree, probiotics are useful in many situations, but they don’t cure everything. In fact, probiotics that contain prebiotics make SIBO worse because the prebiotics start to ferment in the small intestine.

  5. I just read “The Coconut Oil Miracle” which lists microbes that are killed by contact with coconut oil. The fatty acid/lipid content dissolves the coating on the microbes causing them to disintegrate. Don’t know if that bit of info is helpful?

  6. You both always amaze me! Your love for each other, your determination to figure things out, as well as your willingness to keep trying challenging new ideas. Really, I am inspired and motivated everytime I read your blog posts! I thank you sincerely for sharing your journey. It gives me the hope I need. Thank you!!

    • Thank you, Anna. On bad days it feels like all we have is the commitment we’ve made to never stop trying things. And I agree with you, it really helps to have such a supportive community of people who are on the same path: experimenting & sharing ideas & results, so we can all learn (& stay hopeful) together~.

    • Perhaps! I’m sure we could get our hands on some antibiotics (& expect we will probably need to). So funny: black market antibiotics! But right now Matthew is making progress on the strict dietary protocol, which is still having beneficial (rather than negative) side-effects. Negative side effects have been a major complication in his healing: if they are listed anywhere in the small print, he gets them. So he’s going to see how far he can get using a dietary approach, which will also enable him to gain strength for an antibiotic treatment. Thanks for problem-solving with us, Megan~.

  7. Petra,

    You are one amazing lady! I’m sure Matthew reminds you of that often but as friend I want to let you know that your resilience, courage and tenacity is inspiring.

    Thank you for providing such a balanced post on SIBO. It’s nice to see all the information laid out so neatly.

    On a personal note, I’ve restricted carbs and started treating my suplhur intolerance with Dr Yasko’s protocol. I’m not sure if it’s one or the other (or a combo of both) but my sulphur intolerance is improving markedly and my tolerance to FODMAPs is improving steadily.

    I believe that whether diet can ‘cure’ SIBO is irrelevant for the moment because it can clearly improve symptoms, which in turn improves Matthew and your happiness.

    Keep up the great work!

  8. I’ve found that dealing with unhelpful (they didn’t cover that in med school so it doesn’t exist) docs is so frustrating that for things like this overseas pharmacies are the only way to go. They do require a prescription, it amazing how easy it is to write up in a word document with a copy & paste of an apothecary symbol something that looks like your own dr.s script. They never contact your doctor and whether you write it for 1 refill or 10 refills they will refill it forever. Just google how to write a script abbreviations like q.e.d etc. & fax it off. This pharmacy is totally trustworthy I’ve been using them for years.
    That is the link for their generic Rifaximin. I’ve been using their generic Diflucan anti-fungal along with the oregano oil, pau d’arco tea, coconut oil etc (basically everything natural on the candida diet cleanse site to treat the candida that has crawled its way up into my mouth causing horrible burning tongue. It has been so amazing to be able to eat something that has pepper on it. I used to use siriacha on everything.
    D.Y.I. & good luck !

  9. Petra – You are one resilient woman, my friend. Unfortunately, I have no answers for you on SIBO. I only wish I did.

    What I can do, is endorse your book unreservedly. Your thoughtful and pragmatic approach explains biohacking in such an achievable way. It answered questions for me that I wasn’t aware I had, and has given me a more more measured way of dealing with my healing – qualitative and quantitative. Thank you.

  10. Feel a bit daft suggesting anything – your knowledge base is vast! But, if the small intestine specific flora were significantly increased, could they perhaps “crowd out” the interlopers?

    • Brainstorming is good~! That would definitely be an asset-based approach: supporting what we want rather than focusing on what we don’t. My guess is that if that worked, it would be a recommended approach. The inappropriate bacteria that end up the small intestine are incredibly tenacious & have a tendency to armor themselves as biofilms: they group together & produce a protective matrix that shields them from interference. Therefore part of SIBO treatment involves addressing biofilm shielding, so that the more vulnerable bacteria inside the biolfims can be dislodged from the small intestine. It’s so weird to think of these epic battles (& fortresses) inside our guts!

      • Thank you for your detailed reply. I had no idea that bacteria could behave in this way. Tricky buggers…

        I’m always bowled over by the intelligence, passion and perseverance you apply to the pursuit of good health. A true pioneer!

  11. Thank you for this post on SIBO. I have it and did take the course of Rifaxim (which made me feel incredibly nauseous) followed by 10 weeks of Berberine. I still have SIBO. I have to control it with the AIP/Low-Fodmap/SIBO diet, which, as you know, is really restrictive. I am terribly underweight so wish I could feast on carbs! I just heard Alison Siebecker speaking with Trudy Scott on the Anxiety Summit; it turns out they both have SIBO and have not been able to “cure” it with herbals/antibiotics, so they both manage it with diet. Siebecker mentioned that trials have shown that the herbals are now considered as effective as the antibiotic, and she has posted that information on her website. Dr. Kharazian recommends gargling, stimulating the gag reflex and coffee enemas to help restore the migrating motor complex. Siebecker’s site also recommends LDN as a follow up treatment to the antibiotics/herbals, which my naturopath was not inclined to do. I don’t know if that would have helped.

    • Thank you, Jennifer. It is so helpful when we can share information with each other like this. Our collective understanding of SIBO is new. As long as we continue to experiment & share the results of those experiments with each other, I think there is reason to be hopeful that we might find some strategies. I wish you could feast on carbs (at least avocados & broccoli!) too. Maybe it is worth considering the Low Dose Naltrexone as a follow-up treatment if you decide to do another round of antibiotics? As for the enemas, that would be ironic for someone like Matthew, who loves coffee so much, to reinstate coffee through enema treatment, when his protocol doesn’t allow him to drink it~. One way or another, I guess!

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  13. I follow your posts with interest. I too have had severe, debilitating nausea for the past year. At first, I also had severe digestive and joint pain, but AIP took care of that. But still I continued to suffer with the nausea and extreme exhaustion. My job had to be put on hold, and my social life had become nonexistent. I have had Hashimoto’s Disease for 35 years (since I was 15), endomitriosis for 25 years, and have recently been diagnosed with Rheumatoid Arthritis and mild Crohn’s Disease. Since I wasn’t getting better, a month ago, my husband and I decided to spend the money and take me to a Functional Medicine Dr in the San Francisco Bay Area close to where we live. She did about $9000 worth of testing (which my insurance partially paid for thankfully), and I get all those test results on Thursday of this week. But just from my symptoms, she is sure one of my problems is Histamine Intolerance. For HI, I had been eating all wrong. Leftover meat (the worst offender), bone broth that had been cooked over 6 hours, spinach, collard greens, chard, strawberries, citrus fruits, canned fish all make me horribly nauseous I have discovered. For the past three weeks I have been eating low histamine, and my nausea is almost completely gone. I still get fatigued but not nearly like before. I almost afraid to be too hopeful, but my transformation has really been amazing. On Friday, I cleaned my entire house, planted 5 flats of flowers, and was dressed and ready to go out when my husband got home from work. He said, “Where is my wife, and what have you done with her?!” Another thing Dr Mielke suggested was Helminthic Therapy from It’s a bit drastic, but it seems to have done me good. Anyway, I figure if we all share our stories about what is working for us, maybe it can help someone else. I had read about Histamine Intolerance but didn’t think it could be my problem because I had read it is always characterized by debilitating diarrhea. I have always had the opposite problem, but come to find out, HI causes motility problems in general. 25% of people with HI are chronically constipated. Maybe, just maybe, my success can help someone else. Thanks for your posts. I have come to regard you as a friend. 🙂

  14. Oh I meant to add, apparently Histamine Intolerance can be the root cause of Multiple Autoimmune Disease Syndrome, which of course, I have. I am hoping that if I get my histamine levels under control, I will stop getting autoimmune diseases. I am now AIP and low histamine. I still have to restrict a few high Fodmap foods. I had not had a single successful reintroduction in the 10 months I ate AIP, but in the past month, I have successfully reintroduced several foods. It is very exciting!

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  17. I love your blog, it’s helpful and inspiring 🙂 I’ve been sugar-free and avoiding all foods with the most potential for sensitivity for months and it has helped but I’m still looking to fix my constant headaches (and the low energy and mood would be nice, too). Keep posting, please!

  18. My SIBO has resolved after two years on the Specific Carbohydrate Diet. Used Digestive Enzymes, Probiotics and acupuncture. I am so grateful. And love your blog.

  19. I too have had debilitating nausea along with my autoimmune issues. After a year of AIP, lots of other issues were much better, but I still had lots of bloating and nausea. Two months ago, I was diagnosed with autoimmune Ocular Rosacea. Apparently OC is closely related to SIBO. That led me to the Fast Tract Diet, which has truly been a miracle for me. Norm Robillard authored the diet after considerable research into fermentable carbs. You might want to look into it for Mathew. Best wishes!

    • Hi Gina, I had a look at the Fast Tract Diet just now and it seems to be a variation on the gut-healing diet theme. I’m so glad it worked for you~! And thank you brainstorming with us. Like other healing diets, it looks like the Fast Tract Diet limits Fructose, Lactose, Fiber (such as from whole grains & legumes) & sugar alcohols. It also limits Resistant starches, which Matthew can’t tolerate either.

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