10 Reasons Your SIBO Is Not Healing

Auto Immune Paleo, Blog

Oh SIBO. Aren’t you just the party guest we wish would leave? SIBO is short for Small Intestinal Bacterial Overgrowth, and it is a pain to deal with. It can be the pesky bugger behind bloating, constipation, leaky gut and gas. It is also hard to approach as a practitioner because there are so many factors that affect it. From a physiological aspect it is caused by an imbalance in bacteria. Too many of the wrong kind of bacteria reside in small intestine that supposed to be in the large intestine wreak havoc. Gas, bloating, leaky gut and bowel movement issues can come from SIBO. What causes SIBO? It is a long list. Illness, stress, trauma, infections, autoimmune disease, alcohol, hormone imbalances, food allergies..all can contribute. Beyond what I list below, is a SIBO plan or protocol. I did not include a protocol here. Your practitioner should have a host of options for you to help with SIBO (and I am happy to help you too!). But often I only see about a 50% cure rate (that is my own anecdotal evidence) and even in cases of seeing excellent results, I see relapse rates higher than I am comfortable with. So, perhaps…consider these reasons I have listed if you are not improving on your SIBO protocol. I created this list because I saw “perfect performers” not healing.  In the toughest cases, I have found the emotional/belief component is the leading force preventing healing. Did everyone hear that? Emotions, unresolved trauma and stress could be at the root of your SIBO. And that is the good news. The very thing that is preventing healing is the gateway to the healing. Illness is always our opportunity.

1. You have a co-infection

I consider SIBO to be a form of a co-infection. But you can have more than one co-infection at the same time.  H. Pylori? EBV? Cytomegalovirus? All must be addressed. If you have parasites for instance and you try to solve SIBO, it probably will be slow going. The name of the game is to figure out which thing to tackle first and why.

Here are some links to labs I like that do co-infection testing

Diganositics Solution Lab

ImmunoSciences Lab

I love this graphic from ImmunoSciences Lab:

Screen Shot 2015-09-08 at 8.31.31 PM

2. Your cortisol is dysregulated

If your cortisol is dysregulated, it is pretty much like saying “hey you have no gas in your gas tank.” Why do a SIBO protocol when you are running on fumes? I suggest supporting the adrenals for a bit first and then tackling SIBO. Of course you won’t get super far regulating your cortisol with SIBO, but I always say put gas in the gas tank first. You cannot deplete an already depleted person and expected good outcomes.

3. Your blood sugars are dysregulated

This can be related to cortisol quite a bit. But intermittent fasting can help,  (please don’t try that without a doctor helping you) and so can increasing your starchy carbs/fuel as well as liposomal curcumin and resveratrol. Micronutrient deficiencies can come into play here too. I see insulin resistant hypoglycemia all the time. There are many reasons for it, and once you know that you have it, it is easier to heal it.

4. You are not eating Low FODMAP at the right time during your SIBO protocol

If you eat low FODMAP when you are killing the SIBO bacteria, it can be counterproductive. You want the bacteria to be active and present so that the antibacterial protocol can work. I do not recommend starting Low FODMAP until you are done or almost done with your herbal or prescription antibiotics

5. You are eating resistant starch and have an autoimmune disease and SIBO

Resistant starch can contribute to certain autoimmune conditions. My book The Loving Diet will go into detail about this, so grab a copy next month 🙂 And here is the downside: most AIP ‘treats’ are made with foods that are high in resistant starch. Boo!

6. You are eating AIP foods that you shouldn’t be

I cannot stress this enough. While doing elimination/challenge tests work, I prefer the quicker, less stressful route. Cyrex Labs Array 10 is the most up to date testing (in my opinion) to look at immune reactions via ELISA testing and I consider them to be an amazing option. I see so often those on AIP with odd reactions like ginger and lettuce. That means ginger and lettuce should be eliminated from your diet. Healing your immune system, and having a well functioning immune system is key to being ready to clear SIBO. You can go beyond the basic framework of AIP and individualize it. I am always about the quickest, easiest, most loving and logical path.

7. You have beliefs about safety and security in your life that are inflammatory and limiting

Most of these reside in our unconscious, so it is best to get help with them. But Ho’ponoponopono is a great resource for staring the ball rolling on this. When you have stressful or traumatic experiences in life (and we all do) then to make sense of them, we make up beliefs about life. For instance: “life is not fair.” If nothing is done with that belief, then it becomes part of us (move into the unconscious) and will color how we live and decisions we make.. Forgiveness, gratitude and love are three very effective ways to clear held beliefs. Half of my professional work now is helping clients resolve beliefs that are not true through loving, and it can have profound impacts on physical health when we look at healing our life along with healing our bodies. I have found SIBO a wonderful gift in this regard. It is a wonderful opportunity to resolve what is not true in our lives.

8. Your Vagus Nerve is not doing its job due to physical and emotional trauma and stress

We know that low vagal tone affects motility in the gut. We also know that trauma can affect vagal tone (see the Polyvagal Theory). There are some straightforward physiological aspects of healing SIBO that help regulate vagal tone like probiotics. But, there are also a host of ways to increase vagal tone: yoga, diaphragm breathing, increasing Heart Rate Variability, gargling, singing, mindfulness, meditation, exercising and fixing leaky gut. Personally I think the vagus nerve will be emerging to be a big player in the mind-body movement as an interface between the physical and emotions.

9. Your Heart Rate Variability is causing sympathetic nervous system dominance

If you are sympathetic dominant, then it is a bit like you are in fight or flight too much, and more prone to the negative effects of stress and worry. Too much time in the sympathetic state will slow how quickly you heal. But, you can do your own version of biofeedback to balance the autonomic nervous system with Heart Rate Variability measurements. If you measure your HRV, you can track how well you are managing your sympathetic and parasympathetic nervous system. This is fantastic for knowing which days are best to exercise, train, meditate and relax. Very, very useful to healing the immune system, gut and SIBO.

Robb Wolf’s article

Paleo Hacks great article

10. Your autoimmune pathways are not being regulated

NF-kB is a protein complex that controls the transcription of DNA. It is a starting point of inflammation in response to cytokines from autoimmunity. Often with autoimmune disease, NF-kB is activated. But, when NF-kB is downregulated, immune pathways that include Th-1, Th-2, Th-3 and TH-17 are regulated as well. My favorite way to help regulate immune pathways is liposomal curcumin and resveratrol.


  1. Lorena

    Thank you for this information! Do you have any recommendations for carbs that you can eat while doing the SIBO diet? I was eating resistant starch on AIP in hopes of gaining weight!

    • Jessica

      Hi Lorena! There are carbs on a low fodmaps diet, but not a whole lot in each serving. So I recommend you eat root vegetables, and be sure that you eat enough of them…so you may need to increase how often you eat if that is not bothersome. Often it is. If you look up “low FODMAP’ diets online many will pop up that you can choose from that have carbs in them. If you search Specific Carbohydrate Diet there are even more! Hope that helps! -jessica

  2. Sarah

    I just have to comment at how awesome- and much needed!- this article is. Specifically the pieces on beliefs, the vagus nerve, and sympathetic nervous system dominance. Needs to be talked about more, I also believe it is key! Thank you.

    • Jessica

      Hi Sarah! Oh I am so happy it was helpful to you!! I hope that emotional connection catches on more. It may help people get better, quicker 🙂 -jessica

  3. Cal

    Hi Jessica, been on your mail list awhile, bless your want to heal and help people through nutrition, I’m on that bandwagon now. I’m working so hard on health, I have plenty of symptoms and they already scoped me up and down, even talked me out of a healthy organ (GB), then they alienated me, but my most basic symptom is it hurts in the liver area 1-2 hours after eating, that would be when the food is in my small intestine? Never been overweight, O- High metabolism, active, and now it’s a struggle to keep it on in fact. I have a pretty bad past of not taking care of myself, always felt better in the summer because I hit the local farmers markets for foods grown in real dirt (now I’m a gardener three years), The taking care of myself aspect all changed. Hair tests over the last three years show poor mineral absorption, finally got my metals under control! I’m thinking small intestine, what do you think? I am really slowly getting better through a near vegetarian diet and bone broth/stock that I make veggie soups out of, measuring my progress, very slow, but I’ll take it, I mean, hey at least I’m sleeping at night with more nights pain free, and not crying every day, for awhile that was my measurement of progress, pain so bad I’d just go find a quiet place to just cry it out. After they yanked my gb out for no reason I cried every day for a year in pain, almost didn’t make it, for most of last year all hope was lost. Then, I started working on gut health, and have become a mini-expert on the subject, but still, outside of treating for leaky gut, I sure would like some kind of hint. I’ve met some women on FB with same symptoms, none of us really know what is wrong with each other, I’d love for us all to celebrate knowing a little more than we know now, we suspect candida as well. Really, that’s all I could so is go out and find people with the same symptoms, and the candida support group on FB is where I found similar symptoms.

    • Jessica

      Hi Cal! You have been going through quite a bit! I can’t say here on the blog what may be the culprit. A doctor will have to do that, but I will say in regards to the other things you mentioned that healing does take some time. But I really loved your comment and kindness and I am sending love and support to you! Blessings. Jessica

  4. FELICE Hursh

    Thank you so much for your article and yourkind, gentle and loving approach. I have SIBO and a recently diagnosed ulcer. I’m struggling with which to treat first – the protocols are so different – and I know that some of the things to do for each makes the other worse. The old catch-22! To make things worse I have childhood PTSD so I’m struggling, and slowly learning to cope with the long held beliefs you describe. Any advice on which to treat first? P

    • Jessica

      Hi Felice! That would be up to your practitioner. I will say however, that you can’t do much with an ulcer, so that may be worth chasing first…
      Let me know how it goes!

  5. Jennifer

    I have compound heterozygous MTHFR C677T mutation and A1298C mutation. I treated for a short while but without much supervision and so I stopped. I’m wondering how to tie that in with all this complex healing. I haven’t seen you write about it much, but it’s a HUGE piece to the puzzle. Do you work with that also?

    • Jennifer

      Also, pertaining to #4, I’m slowly re-eliminating foods (years of yo-yo elimination and treating), to get more in balance with a happy gut and help improve my mind/nervous system, but I’m remembering why I stopped eating low FODMAP diet – I didn’t feel the restriction of more foods while I wasn’t actively treating was a healthy diet and it caused an immense amount of stress. How do you recommend eating low FODMAP on addressing health complexities on diet alone (I have appts coming up to slowly re-enter treatment protocols) when not actively treating on supplements and herbal antibiotics currently?

      • Jessica

        Hi Jennifer! I don’t talk much about MTHFR because I am not an expert in it. There are SO many wonderful resources (a fabulous MTHFR facebook group for example) run by Carol Savage and Amy Yasko’s work. And of course Ben Lynch. Even since writing this post, many things have changed. I have found chronic co-infections can drive SIBO. And the emotional and relationship connection we have to our life can stall any SIBO protocol. So I start there with my clients and examine their connection to life and beliefs around it. SIBO will not heal (in my opinion) otherwise. And I agree, low FODMAP is very, very hard. So that is another reason why I encourage my clients to first take a mind-body approach or at least include it at the beginning to help assist with stress. I find SIBO protocols with out the mind-body piece are somewhat ineffective as they do not really address the root cause which tends to be safety, security and trust. Hope that helps! -jessica

        • Jennifer

          Thank you! I am so looking forward to working with you!

  6. Amy

    Another virus not talked about much but I believe also contributes to autoimmunity is Parvovirus B19 (also known as Fifths Disease or slap-cheek disease). It is generally a childhood virus that passes without much incidence – except for those of us with immune system difficulties. I am going to undergo an antiviral regimen in the next few months to address my nearly two-year battle against Parvovirus B19. Most doctors don’t recognize it as a problem. It can be very frustrating. Thankfully, I think I may be on the right path finally.

    • Jessica

      Thank you for sharing this Amy!! -jessica

  7. Ann

    With all of this listed as to why sibo is nto being cured , what is a person to do when they’ve been tested, taking herbal combination via functional medicine, tried sibo diets, food maps and all of the others but to no avail? I am so confused! The stressors dominates everyday life i.e. what to eat and not to eat. How does a person get rid of this?

  8. David


    In regards to #4, I’m a bit confused. Why would I want to “not eat low FODMAP while I’m taking supplements to kill SIBO? It sounds very counterproductive to do it the other way actually… starving the bacteria and killing it would be productive. Why would I want to feed it, causing proliferation while I am trying to kill the overgrowth at the same time?

    Could you clarify for me?

    Many thanks.


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