My Story with SIBO / The Need to Experiment / Trying to get Rifaximin

Unfortunately we can’t always know exactly what is happening in our gut. Back in September my current family doctor was kind enough to humour my protests that gut issues, not stress, were the source of my health problems. She ordered a battery of diagnostic tests, including a barium enema, a small bowel follow through, a gastroscopy and a colonoscopy. These tests are useful to detect major abnormalities in the gut, including significant structural abnormalities, swelling of the intestinal wall characteristic of inflammatory bowel diseases (such as Chrohn’s and ulcerative colitis), cancer, and even celiac disease. Testing can also be useful to draw biopsies from the GI tract, which can subsequently be analyzed to confirm the presence or absence of potentially pathological microbial strains such as H. Pylori. Barium enemas in particular are useful if you’re someone who appreciates safe and mildly erotic ways of being tortured. Over the next eight months (thanks Canadian health care) I would perform each one of these tests. They didn’t find a single thing wrong with me. Although this didn’t exactly help my cause in trying to identify the origin of my illness, these tests did remind me that things could always be a lot worse. Despite how long it took I’m still glad I got it out of the way, and I’d recommend the same for anyone else, at the very least to eliminate the more serious possibilities out of the many others that could be contributing to whatever symptoms they’re experiencing.

When it comes to health problems that primarily stem from dysbiotic gut bacteria, aside from the more common infections alluded to above, these tests tend to be unhelpful for detecting the issue at hand. Naturally though, as nothing abnormal was found, the doctor will then tell you everything down there is perfectly healthy and therefore your symptoms are due to psychological stress. The reason you should take this diagnosis with a grain of salt is because the science, medical technology, and knowledge of most doctors regarding the gut microbiome isn’t advanced enough to the point where we have universally agreed upon tests that can detect every possible abnormal manifestation of bacterial colonization in the gut. The current tests used by doctors are inevitably going to fail to identify the root problem for someone with say, irritable bowel syndrome. And that’s exactly what irritable bowel syndrome is – a wastebasket diagnosis given to someone who is experiencing gastrointestinal issues with no clear cause identified by the tests mentioned above. It’s the medical way of shrugging your shoulders at a patient. That doesn’t mean that IBS has no cause, it just means that the medical community has not yet adopted a surefire way of detecting and diagnosing it. There’s no standard for them to measure it with an instrument and say, hey, that’s IBS.

That doesn’t mean your desire for a diagnosis is hopeless. There is a rapidly increasing amount of useful and accessible scientific research that can at least provide a patient with some sound ideas of what may be going awry in their gut, if they’re willing to do the legwork. If you are truly ill and modern medicine can’t provide the help you need, the solution is not to just do nothing and accept your fate. Doctor’s don’t have time to become an expert in every single field of health and disease – particularly when it comes to nutrition and microbiome research, you can become far more educated and knowledgeable than most doctors are in pretty short order if you work at it. On top of that doctors operate under certain restrictions and guidelines that you don’t – you can form hypotheses and experiment with treatments in ways they can’t. Read the scientific research that is available and form an educated theory on your own, or if possible, with the help of a knowledgeable practitioner. Then find (safe) ways to test it out. Analyze your results, do more research, modify your theories and retest them. Do this over and over and over and in time you’ll get closer and closer closer to finding the root cause of what’s making you sick. You’ll find eventually that your understanding of your own health issue correlates directly with your improvement. It could take years, but it’s a lot better than doing nothing.

Anyways, by doing just that I’ve become pretty certain I have small intestinal bacterial overgrowth, or SIBO. I first suspected I might have SIBO about a year ago after having bad reactions to a certain probiotic given to me by the naturopath I was seeing at the time. As it was early on in my learning curve with gut issues, whenever a gut-targeted supplement that was supposed to make me feel better was temporarily making me feel worse, I would (wrongly) always attribute it to a Herxheimer reaction, aka die-off. My naturopath convinced me of this and I didn’t have the knowledge at the time to disagree with her. After a few months of banging my head against a wall taking this treatment that was actually making my symptoms worse, I decided to experiment with a different probiotic to see if it would have the same effect. In contrast I tolerated it pretty well. I then decided to take a closer look at the ingredients list of the probiotic that was giving me issues and noticed the addition of FOS, or fructo-oligosaccharide. A quick Google search identified FOS as a prebiotic, which is something that when consumed, promotes the growth of healthy bacteria in the gut. This would normally be a good thing, but for someone who already has an overgrowth of bacteria in their small intestine, consuming prebiotics generally exacerbates symptoms. At that point I thought it would be worth it to investigate whether I may have SIBO.

Patients who have SIBO usually have difficulty with high FODMAP foods (FODMAPS = fermentable oligo-, di-, mono-saccharides and polyols). I decided to eliminate these foods and overall my symptoms improved. After a few days I re-introduced them and starting from 5-10 minutes after my meal, I became bloated, my head pressure increased, my brain fog increased, my mood worsened, my energy dipped, and I got pins and needles in my feet. These symptoms would get worse as the day wore on. After letting my body recover for a couple days I would then then experiment with eating different types of FODMAP foods, and without fail each attempt produced the same symptoms. This included any fruits, due to their higher fructose content (even low fructose fruits produced the symptoms, although not as severely).

(Note: if you suspect you might have SIBO and are looking for information regarding which foods are safe/unsafe on the low-FODMAP diet, the Monash University Low Fodmap Diet App is a really great and easy to use source. The university is continually testing foods for their FODMAP content, so the app is always kept up to date. Unfortunately they do charge to download the app, so if this is a problem a free, quick and dirty online source to use instead can be found here: )

What was also interesting is that these FODMAP food reactions were very different from my more obvious and severe reactions to foods like gluten, dairy and egg, which to me indicated that my body was likely having negative reactions to this class of foods through a separate mechanism.

I decided to get tested. In May 2016 I found a new naturopath in Toronto who actually had experience dealing with SIBO patients and could order the lactulose breath test for me through Geneva Labs. Sure enough my testing came back positive for hydrogen-predominant SIBO. This still isn’t a definitive diagnosis as these tests can occasionally generate false positives and negatives, but I figured that along with my symptoms and sensitivity to FODMAP foods, getting treated for SIBO would be a good idea. If I showed improvements, it would further add evidence that I actually might have SIBO. If I showed no improvements, there was a good chance I could eliminate SIBO as a potential factor affecting my health.

This naturopath treated me with a garlic extract (Metagenics Supergarlic 6000) and a supplement called Candibactin BR, both of which are antimicrobials that have been shown in research to be effective against SIBO. It improved my symptoms a lot the first few weeks until I hit a point where I felt almost completely better for the first time in a very long time. But then things got worse again. Then it would get better, then worse … and it kept cycling back and forth like that. Based on my initial improvement I was convinced that I struck near the root of the problem, but for some reason I couldn’t sustain that symptom relief. I figured there must be something else I wasn’t addressing, so I got off the supplements temporarily to figure out what that was.

My diet was the obvious first place to look, as I figured that if I wasn’t working to improve the health of my gut flora through eating a proper diet then the SIBO would inevitably return regardless of whether I successfully killed it off or not. At the time I had a very limited selection of foods to choose from with all my sensitivities, and I relied on eating copious amounts of meat to get enough calories for the day. Besides that my only safe foods were olive oil and boiled bell peppers, zucchini and bok choy. At some point I started taking a different probiotic called VSL #3 that helped me tolerate many more vegetables as well as quinoa, which allowed me to reduce my meat intake and eat a more balanced diet. This in and of itself helped my symptoms dramatically.

I then decided to give the antimicrobial supplements another try, but did things a bit differently this time around based on some studies I had read. First, I used Candibactin BR and Candibactin AR as my antimicrobials of choice, as this combination had been shown in one study to be at least as effective as rifaximin (the typical antibiotic of choice for hydrogen-predominant SIBO) in eliminating bacterial overgrowth. Second, based on information disseminated online by one of the leading SIBO researchers in Dr. Pimentel, I consumed small amounts of FODMAP foods while taking the antimicrobials. The basic idea is that keeping the bacteria fed and happy prevents them from creating the protective defenses used to help them survive under starvation conditions, thus making it easier kill them off.

If I still couldn’t maintain symptom relief through this attempt, I would instead try and get a prescription from my doctor for rifaximin in hopes that I could nuke the SIBO into oblivion. Although rifaximin is relatively benign compared to other antibiotics, going the antibiotic route was not really something I wanted to do unless I had to. Herbal antimicrobials tend to spare some of the good bacteria while antibiotics have broader action, so I wanted rifaximin to be my last resort.

However this time around the herbal treatment worked like a charm, and I was able to get back off of the supplements in just three weeks. Throughout the treatment I slowly and cautiously worked up my intake of FODMAP foods while simultaneously taking 1 candibactin BR 3x a day and 1 candibactin BR 2x a day. By the end FODMAP foods became a staple of my diet. All of a sudden my diet had increased dramatically in the number of foods I could eat, and with these prebiotic foods in my diet I was feeling better and better every day. My gut felt a lot better, I felt happier and more relaxed, more excited about life, more willing to go out and hang with friends, and my brain fog was gradually disappearing.

This lasted for about four happy months until I slowly started to become more sensitive to FODMAP foods again. Dammit. I tried going back to a low FODMAP diet again which helped initially, but after two weeks I started getting terrible anxiety and fatigue. Interestingly, if I consumed just small amounts of FODMAP foods afterwards, these symptoms would dissipate very quickly. I think that the bacteria in my gut had adapted to FODMAP foods in my diet and weren’t willing to concede them completely all over again. This actually brings us to today, April 18, 2017, where I’ve been eating tiny amounts of FODMAP foods daily for the past couple weeks to strike a balance between keeping my gut bacteria somewhat content while keeping my FODMAP reaction symptoms as low as possible.

The above probably seems like an unnecessary amount of detail. The reason I decided to include it is because:

a) I wanted to post my experience for anyone else who suspects they might have SIBO
b) I wanted to show how it’s possible to think critically about one’s own illness and symptoms to narrow things down to a root cause, and by doing so improve the condition of their health on their own accord
c) I believe that before you try any treatment, especially if it involves modifying the bacteria in your gut, you should develop a pretty strong rationale for doing so first. I.e., you should develop a good hypothesis of what the problem is and why your proposed solution might work. No matter how bad things are, they can get worse if you just start putting things in your body at random. The first naturopath I saw for my gut-brain issues wanted me to buy a $500 box of supplements that included a wide assortment of natural and homeopathic remedies, and in my desperation for a quick fix (being in the thick of school) I complied. She claimed to have a lot of experience treating patients with my exact issues, and that she’s never dealt with a case that she couldn’t fix. As long as I did what she said, she assured me, I would get better. The first day of taking all of the supplements, I legitimately felt like I was going to have to go to the hospital. I felt horribly dizzy, nauseous, faint, depressed, and foggier than ever. She was surprised at my reaction and said that it must just be a strong die off reaction, and told me to instead take just one of the supplements in the box (i.e., the probiotic with FOS in it) until I gained tolerance, then slowly reintroduce the other ones one by one. She told me it would take a long time before I see significant improvements, and my stubborn faith in her lasted for 7 months. Desperation can make you do stupid things. Moral of the story – be patient and form a smart, well-thought out plan before trying any treatments that could potentially make things worse. Get informed. Be your own scientist, and then be your own doctor.

Today I am going nuclear. I’m about to see my family doctor to try and get a prescription for rifaximin, in hopes that I can clear what I strongly believe is SIBO in relatively short order. I have a masters program starting in a month and so I’m hoping to dear God the antibiotic works. The deal with my doctor back in September was that if all my GI testing came back clear, I would be awarded the diagnosis of IBS, again otherwise known as “I don’t know”. But more importantly, she would then *maybe* reconsider my request to try rifaximin. I will keep the blog updated with how that goes.

If I do get the rifaximin prescription, I’m planning on documenting my experiences from start to finish for anyone who may be considering rifaximin in the future. More on that soon.


3 thoughts on “My Story with SIBO / The Need to Experiment / Trying to get Rifaximin”

  1. How did your treatment with the antibiotics fare? Did you relapse again? I have been using Candibactin AR/BR for a methane-producing infection. Finished a 6-week course and in just 2-3 days symptoms are returning again. Curious your experience going the nuclear route…


  2. Hi Jacob. Sorry for the delayed response, haven’t been on this blog for a while. Unfortunately I had a bad experience with it overall. My symptoms cleared up for about 4 days which was promising, but then my symptoms actually got worse than they were before I took rifaximin. I was in pretty rough shape for a while and it took about 4 months to get back to normal. Just out of curiosity, what are your symptoms?


    1. Hey!

      Thanks for the response, and I’m sorry to hear it didn’t go well for you. I had just visited Mexico in December of 2017 and I drank or ate something from a restaurant that must’ve been unsanitary. That night I immediately started experiencing sweats and pain in my lower left abdomen, with some pain around other parts of my intestinal tract here and there. I couldn’t even sleep that night. It started as problems digesting and sensitive bowls those first few days and then only worsened. Each morning after that first few days of pain was accompanied by INSANE volumes of gas which were painful, and multiple visits to the bathroom with very unformed stool. Lethargy, nausea, dizziness, sweating, lack of motivation, and elevated heart rate were my main symptoms. I finally had a stool sample taken and found out I had definitely picked up fusobacterium while in Mexico. I just finished my 6 week course of Candibactin Ar/Br 2 weeks ago. I have not had the same problems, however eating many foods I can no longer break them down anymore. I initially thought my symptoms were returning when I ate some items considered to be HIGH on the FODMAP scale, but eliminating those foods immediately reduced the gas and pain I was having. In my estimation, I’ve eliminated the main invader, but have very few bacteria left that are good at digesting fermentable foods. I plan on eating homemade sauerkraut to replace those bacteria that are known to do this well. I’m definitely feeling much better but it did take me about 6 months to go from initial infection -> self-treating with stuff I thought would work -> testing -> candibactin regimen -> now. Hope this helps.


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