I feel like everyone remembers the moment they received their SIBO diagnoses. After dealing with the incompetence of conventional MDs who were adamant that “it was just IBS,” I felt a wave of intense gratification when my functional medicine practitioner diagnosed me with SIBO. All my intuitions that there had to be a cause for my GI complaints were right! And who doesn’t love being right, especially when it seems like the whole world just thinks you are crazy.

The SIBO diagnoses seemed like the answer I had been so desperately looking for. It gave me hope by giving me a place to start. My functional practitioner reassured me that I should be feeling much better after we cleared the bacteria from my small intestine. In my mind, I had found the root cause of my issues and I was ready to dive into treatment.

But, after months of FODMAPing, antimicrobial agents and continued research, I realized that focusing on  bacterial clearance didn’t come close to resolving my problems. In fact, many of my issues seemed worse than ever. I was beyond frustrated.

At this point, my mindset changed. What if my SIBO wasn’t the root of my health woes, but rather a symptom? I realized that I needed to put my detective cap back on to figure out the root of my SIBO. I think treating SIBO as a diagnoses is a huge problem in both the conventional and functional medicine communities right now.

The 3 Main Problems with treating SIBO as a diagnoses (and not a symptom):


Problem #1: Not focusing treatment on correcting DELAYED MOTILITY or dysfunctional Migrating Motor Complexes (which is at the heart of almost all SIBO cases).

The MMC are cleansing waves that stimulate peristalsis in the smooth muscles of our GI tract. More simply put, the MMC keeps things moving, so that foods we eat are not sitting in the GI tract. You can think of the MMC as a housekeeper that sweeps the small intestine clean of undigested food stuff. If the MMC is dysfunctional, SIBO will usually develop and persist until the MMC is addressed. Therefore, SIBO appears to be a consequence of nervous system dysfunction.

By labeling SIBO as a diagnoses, I feel that it has narrowed the clinical focus on the “overgrowth” rather than the disturbances in motility. I think that the medical communities need to start viewing SIBO as a SYMPTOM of a brain-gut axis issue.

Instead, many practitioners and SIBO sufferers focus primarily on treatment strategies that starve and kill bacteria and less on rebuilding the damaged MMCs. Yes, I know many SIBO protocols and treatment plans do use prokinetics, but is this enough? While prokinetics are helpful by stimulating the MMC, they don’t repair existing problems in the MMC. A past food poisoning, IC valve issues, hypothyroidism, liver diseases, stress, colonic dysbiosis, lack of sleep and autoimmunity can all impair MMC function. The MMC disrupters need to be addressed in order to truly repair the brain-gut communication to prevent chronic SIBO from occurring.

Datis Kharrazian is one of the few popular practitioners that focuses PRIMARILY on treating the brain-gut axis in chronic SIBO cases. He recommends exercises that activates the brain and vagus nerve like gargling, gagging exercises and coffee enemas to strengthen the signaling between the brain and the gut to repair motility in the GI tract.

I first heard about vagus nerve exercises for SIBO from my first functional medicine practitioner. The practice would send out tons of information via email that you were supposed to thoroughly review. Being a busy lady, I seemed to have missed the email on the vagus nerve and my practitioner failed to mention the vagus in our conversations that seemed primarily centered on hashing out the FODMAP diet and deciding on an antimicrobial protocol. He brought up the vagus briefly almost as an afterthought in one of our sessions, but I of course was to wrapped up in my battle with the beasties in my small intestine to add anything extra to my routine. In my opinion, brain-gut axis repair should be at the forefront of SIBO treatment, not an afterthought that gets lost in the shuffle.

Personally, I experienced positive results when I stopped fearing FODMAPs and bombing my gut with antimicrobials, but instead focused on my brain and vagus nerve health. I did some hard core gargling exercises in the past and noticed an increase in gut sounds and motility in just a couple of weeks. I felt like my bowels were being turned on after a long hibernation!

I would also like to make it clear that I am not saying that you should ignore the overgrowth completely and only focus on the brain-gut dysfunction. In fact, inflammation from small intestine bacteria can lead to a continual break down of the brain-gut axis. But, in my opinion, we often have horse blinders on the overgrowth and we fail to spend much time at all on the brain-gut aspect. And again, I can’t say this enough, SIBO IS A SYMPTOM of a motility issue! I think in my next post I am going to do a write up specifically the brain-gut axis that will go more in-depth, so stay tuned for that!

Problem #2: Blaming every symptom on SIBO.

I think another problem with a SIBO diagnoses is that many people start to blame everything on the SIBO. I was a very guilty of this. When ever I was hungry, foggy-brained, moody or just didn’t feel well I would blame my gut bugs. You know that Jamie Foxx ft. T Pain song “Blame It on the Alcohol“….well I was blaming everything on the wee beasties in my gut!

By just blaming everything on the gut bugs, I failed to see these symptoms as clues to other problems (in particular cortisol dysregulation, blood sugar and thyroid problems). This was especially true when I went lower carb to try to starve the gut bacteria. I felt horrible, but of course I justified that it was just a die off reaction. I was just making the gut bugs angry. In reality, this shift to a low carb diet caused my already elevated cortisol levels to rise even more and my thyroid hormones to fall leading to blood sugar instability, fatigue, moodiness and brain fog.

As I mentioned above, stress and thyroid issues can delay motility, which can only exacerbate SIBO. I remember craving carbs and thinking “oh that is just my hungry gut bugs trying to get me to crack and feed them.” Even my functional practitioner told me to resist the cravings. But, my body was just trying to tell me that I needed more carbs to support my hormones. By avoiding my cravings, I was only making matters worse.

I also blamed any amount of bloating on SIBO, when large intestine imbalances were actually to blame. Again my functional practitioner seemed to think that any amount of bloating indicated SIBO, which is pretty absurd looking back on everything (I don’t go to that practitioner anymore thankfully).

We can’t treat SIBO in isolation, the whole body needs to be supported in order to eliminate the overgrowth. In my case, other hormonal issues and large intestinal dysbiosis seemed to be responsible for a majority of my symptoms and even my disturbed motility. By narrowly focusing on the overgrowth, you can fail to truly see other problems that need to be fixed.

Problem # 3: Fosters a “gut bacteria is the enemy” mentality in SIBO sufferers leading to overtreatment.

By labeling a bacterial overgrowth as a diagnoses and not a symptom, many sufferers and practitioners alike fall into a “kill at all cost” mentality that can be incredibly detrimental to long term outcomes in treating SIBO. This bacteria is the enemy mentality can lead to abuse of antibiotics and overly restrictive diets, which can deplete colonic bacteria.

As I have mentioned in past posts, large intestine bacteria communicate to the brain to stimulate the MMC. Without a healthy population of colonic microbes, motility will be disturbed and SIBO recovery will be next to impossible. Therefore, there is a narrow window to treat SIBO. You want to reduce the bacterial load in the small intestine without doing too much damage to the large intestine. Relying on cyclical antibiotic treatments and diets to kill and starve the bacteria will usually temporarily take care of an overgrowth, but will also cause long-term issues with motility. We need to support the health of the entire GI tract to achieve a successful SIBO recovery.

If SIBO was viewed as a symptom of a brain-gut dysfunction diagnoses, I think it would be easier to avoid falling into this overtreatment trap. We can’t lose sight of gut bacteria’s central role in rebooting our MMC activity.

Bottom Line:

As a former marketer, I understand the power of words to drive attitudes and perceptions. When we use the label small intestine bacterial overgrowth as a diagnoses, we naturally view the disorder as a bacterial problem. But, usually the overgrowth is rooted in brain-gut axis disturbances (from a variety of different causes). By labeling the disease as a brain-gut disorder, we naturally can focus on the root cause of the overgrowth. I hope in the future we can shift away from using SIBO as a diagnosis.

Thanks for reading!!! I have been crazy busy with school the last couple months, but will be increasing my posts through the summer! So stay tuned!

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  • Funny timing. I was first diagnosed with SIBO (methane) about 1.5 years ago. Then a bunch of other diagnosis followed in rapid succession: hypothyroidism, adrenal fatigue, candida, EBV, parasites, intrinsic factor, etc. etc. My ND had me on a kill herbal protocol combined with a insanely restrictive AIP/low-FODMAP diet, but my body absolutely tanked. Like you, I was all about resisting the call of carbs because of the same reasons you wrote. (As an aside, I absolutely can’t stand when people personify gut microbes and give them human qualities like, “Evil Candida is manipulating you to eat that Larabar so it can feast on it!”) Anyway, I did add in FODMAPS, but stayed clean and felt SOOO much better. Combined with the heavy herbal kill protocol, I beat SIBO….for 3 whole weeks. lol. Then it was back. It’s been a rollercoaster of a year since with lots of up and downs, but JUST THIS WEEK my latest doc diagnosed me with MMC disorder. It was an aha! moment. I have major IC valve inflammation all the time and she believes because it is a regulating valve, it’s setting up a chain reaction where I not only do I have to deal with SIBO, I also have gallbladder and pancreas attacks because everything is backing up. Literally. My question for you is do you know of any protocols to fix MMC besides Vagus Nerve stimulation? I’m working on that one, but what else should I consider? My doc said there is a prescription available from Canada that is an effective pro kinetic, but to me, that’s just a bandaid. And I’m hesitant to take anymore pharmaceuticals. I tried LDN a few months back. I did not do well on it at all. And ultimately, I’d like to get to the root of the disfunction. Any leads on things to look into for IC valve issues? Appreciate your posts! Super informative and down to earth. Thank you!

    • Hi kkate77,

      Thanks for reading! I’m happy to hear you are digging and addressing the root of the issue! As far as your question goes, I am assuming you are thinking of non-pharmaceutical prokinetic agents to help you while you are addressing the root? I have heard some people have some success with Iberogast and MotilPro. Ginger also has some prokinetic action that stimulates the MMC. I know one guy who swears by chewing on ginger root before every meal because the juices can really help facilitate digestion. In my opinion, I would talk to your doctor about trying some of the more natural options first (while also doing vagal nerve exercises). If you are still having a lot of issues than maybe consider adding some pharmaceuticals. But again, this is probably something you need to hash out with your doctor to determine what the best treatment is for you!

      I also know that their are particular massage exercises that you can do to help with the disturbed valve function to make sure you can manually closed the valve via message to prevent bacterial translocation. I am not sure what are the best exercises, but I am doing some research for future blog posts, so I should be posting about that at some point in the future. In the mean time, I would suggest trying to research some good manual massage exercises for the IC valve issues because I have heard that it can really help!

      I’m wishing you well in your healing journey!

  • Thanks so much for the reply. Yes, I’d like to avoid the pharmaceuticals. I just ordered Iberogast and will give it a go as I work on addressing the root cause. My ND closes my ICV each time I visit her and from experiencing what she does, I *think* I am closing it when I try the same at home. But I’m eagerly looking forward to anything you dig up on how to accurately learn how to do that. Besides gargling, gagging, and CE, have you come across any other methods of stimulating the vagus nerve/HPA? One thing I’ve recently stumbled across is the use of a power plate. It’s a piece of exercise equipment that you stand, lunge, plank, etc. on. It vibrates at super high frequency causing your body to have to work harder in a shorter amount of time. But a trainer I know who is certified in using power plates has seen HPA improvement in his clients who suffer with dysfunction simply through use of the power plate. I have to do more digging on this one, but pursuing strengthening vagal tone and HPA intuitively feels right as I march down this healing path. Anyway, thanks again for replying. Appreciate your time! Best, Kim

    • Interesting about that power plate!!! I will have to look into that. I know that yoga and meditation are good additions to help lower stress and stimulate the vagus. I also know that singing and humming can help stimulate it…so I tend to sing loud and proud in the shower or whenever I am in my car hahaha! Best of luck Kim!

  • I couldn’t agree more! I first received my SIBO Dx in 2011. Here I am commenting in 2017 because it shouldn’t be a Dx, but a symptom of some other issue that allowed/caused SIBO to happen. I cannot get anyone to address the underlying cause (which I believe is motility/damaged MMC, I even has delayed gastric emptying so motility makes sense) or help me with prokinetics… and I have paid out of pocket, flown across the country, seen naturopaths and functional medicine physicians, attended the SIBO symposium… It is so frustrating to constantly relapse. Have found more information that might help me since writing this? I am working on vagus stimulation. I don’t notice a difference. Thank you in advance for any further information.

  • I think I have SIBO after repeated antibiotics my symptoms are bloating, gas , burping after any food , loose stools every day 3 months after finished antibiotics , I have been on continuous good quality probiotics since the last day of the antibiotics, but despite that I still continue to have that symptoms, I also lost 10 pounds, I just started FODMAPS diet , but I don’t see much improvement, I also doubled the probiotic dose thinking it will help.Can you please tell me what kind of symptoms you had when you were diagnosed and what is the best
    Probiotics to use , I’m taking Symprove which is refrigerated cultures of L rhamnosus,E faecium ,L plantarum,L acidophilus, I’m also considering stopping the probiotics to see if there is any improvement since I know some people don’t recommend them with SIBO , I just don’t know what to do , I’m so fed up with doctors that I just don’t want to even go and see any at the moment and thinking I just want to treat myself by trying different options, please advise, how you feeling now , have you got any improvement..?