When I was diagnosed with SIBO 5 years ago, I was put on an herbal regimen to clear the bacteria overgrowing in the small intestines. I was also put on a very restrictive diet to starve the overgrowth. Symptomatically, I felt a bit better while I was treating the SIBO, but I still did not feel great.

After 5 weeks on the herbs, I told my functional practitioner at the time that I was still bloated. He told me that the bacteria must still be there and that I needed bigger guns to take out my overgrowth. It also planted a seed in my head that bloating was a good indicator whether I had SIBO or not. I learned the hard way that this is not the case, but I will discuss this a bit later.

This functional practitioner told me to ask my doctor to write me a prescription for an antibiotic. We couldn’t get my insurance to cover the Rifaximin because it was before the drug was officially approved for SIBO. So instead, I was prescribed CIPRO.

Taking CIPRO was the worst mistake that I made in my whole SIBO journey. Unlike Rifaximin, CIPRO is a broad spectrum antibiotic that has a black label warning because of all the negative effects it can have in the body. Being desperate and in pain led me to try this antibiotic, I felt so much worse after it.

After this CIPRO disaster, I was mentally and physically broken. I had done everything right in my mind! I followed a strict SIBO diet and had even developed more symptoms than when I started. The real kicker is that after CIPRO I had systemic yeast issues. I even took some anti-fungals with the antibiotics to prevent the yeast, but the yeast still reared its ugly head anyway.

Looking back at my case and knowing what I learned through my own SIBO journey and working with SIBO clients, I should have never taken that round of CIPRO. I should have retested and started to address my root causes.

But, I (like so many in the SIBO world) became stuck in a kill mentality. I linked all my symptoms to the overgrowth and didn’t look more closely at my root causes. Unfortunately, I thought that all of my symptoms would go away if I cleared the overgrowth. But, I have found in my own case and in my clients that you can still have bloating and GI symptoms after the SIBO is cleared.

Over diagnosis of SIBO

I also believe that SIBO gets over diagnosed. When you present with IBS-like symptoms, many functional practitioners will diagnose SIBO just based off of symptoms and that is a mistake.

Or you may have self diagnosed your SIBO. While you may feel confident that you have SIBO, it is extremely beneficial to work with a knowledgeable practitioner that can diagnose you properly and help guide your treatment. You can end up wasting time, money and energy by failing to properly diagnose the problem.

Large intestine imbalances, fungal overgrowths and h pylori can all cause similar symptoms as SIBO. Hormonal imbalances and brain-gut axis dysfunction can also be a primary driver of gut symptoms. It is a mistake to assume that if you have bloating that you automatically have SIBO.

Practitioners will sometimes still treat even when you have a negative breath test. In some cases, this may be warranted (especially in cases of hydrogen sulfide), but many who test negative on the breath test don’t have SIBO. Antibiotics and other SIBO treatments could aggravate the true problem.

Getting an accurate diagnosis based off symptoms, labs and your history can be key to determining what is the best strategy to clear SIBO and to keep it away.

Once SIBO is properly diagnosed, it can be easy to over treat

Many SIBO protocols are solely focused on killing and clearing the overgrowth. There is less emphasis on how to repair the breakdowns that led to the SIBO developing in the first place.

As I know full well from my own experience, it can be easy to get fixated on killing the bacteria versus restoring balance and repairing root causes. You can start blaming all symptoms on SIBO and fail to see other underlying issues. And by over killing and starving your gut bugs, you can actually create additional problems that you will need to fix.

Looking at my stool tests before the antibiotics and diet restriction vs 3 months after the treatment, there was a night and day difference. I decimated my good gut bacterial populations and also developed several opportunistic over growths that were not present on the stool test before treatment. Not to mention, I was still symptomatic.

With SIBO, there is a narrow window of benefit with antibiotics. You benefit when you can find the sweet spot of clearing the overgrowth without depleting too many of your large intestinal microbes. That is a fine line, but it can be easy to go overboard if you are stuck in a kill mentality.

Doing round after round of pharmaceutical and herbal antibiotics for SIBO can really disrupt the fine balance in your gut. I see many mistakenly viewing long term herbal use as safe, but these can still deplete large intestine microbes over time.

If you are symptomatic, more herbal or pharmaceutical antibiotics is not always the answer. In fact, you could be creating more problems for yourself.

Diet restrictions are similar to antibiotics. They can be helpful at first to control symptoms, but overtime you will starve large intestine bacteria.

Typically, I don’t use a strict Low FODMAP diet unless someone is symptomatic and the diet is controlling their symptoms. I try to not have someone on a low fermentable fiber diet for longer than 6-8 weeks before adding foods back in to prevent depletion of the good gut bugs in the large intestine.

What is too much?

This is going to vary based on the particular case. For herbals, I typically don’t have clients stay on herbals longer than 2 months. But, in rarer cases, 3 months may be needed.

For antibiotics, typically 2 weeks will work, but some cases 4 weeks is necessary. I would try to avoid being on antibiotics for longer than 1 month straight.

If you are still symptomatic after treating, you can re-test to see where your levels are and if you need additional rounds. I tend to be a bit more conservative. You can always do more, but it becomes an uphill battle if you go too far in the clearing phase.

You also could benefit by working on rebuilding and repairing the gut following antibiotics. Here is another post about why you are still having symptoms after treating that might be helpful.

Root cause repair is key during and after treatment to prevent relapse. You can become caught in a vicious cycle of clearing and relapse that can lead to a reliance on cyclical antibiotic use.

Are antibiotics always needed to clear the SIBO?

I believe we need to change how we think about the clearance phase. I have seen certain SIBO sufferers respond really well to targeted probiotic treatment to clear their overgrowth. Especially when the SIBO sufferer has a more mild to moderate overgrowth.

Using the right strains is the most crucial part. I love bacillus strains because many produce antimicrobial compounds that can clear the overgrowth. You can think of them as intelligent antimicrobials because they can attack the overgrowth head on while helping optimize the large intestine environment.

Pairing the right antibiotics and probiotics can also be a more muli-faceted clearing strategy. I see antibiotics/herbals in combination with probiotics being more helpful than the antibiotics alone.

Bottom Line:

You can over treat SIBO. In doing so, you can create more problems down stream in the large intestines. When you have symptoms following a clearing phase it is not always SIBO, it is best to test and not guess.

Learn more about the SIBO Root Cause Repair Program by clicking here.

  • II was diagnosed with Sibo – hydrogen via a breath test. I had several test. I had a small-bowel follow-through and was ddagnosed with rapid transit, or dumping syndrome. My GI feels that this is my root cause.My symptoms are not terrible. Mostly gas and some bloating. Neither diarrhea nor constipation very often, although I’m prone to constipation. I I am now on a 14 day, 3x a day Rifaximin course. The problem is, the diet for dumping syndrome is quite different from the low-fodmap diet. 6-8 small meals a day versus intermittent fasting. Fiber vs. non-fiber, etc. I’d like to follow the low-fodmap diet for 6 weeks, but then I’m not doing anything to treat my root cause (if that IS my root cause!) Any thoughts?

    • Hi Kathy,

      Thanks for the comment. While I do not know your case, I would say that dumping syndrome is more of a cluster of symptoms and not usually a root cause. The question then becomes….why do you have these symptoms of dumping syndrome? I would keep digging for your root causes. Once your root cause becomes clearer, you probably can figure out what diet makes the most sense. I am accepting new participants from my root cause repair program which might be helpful for you. Best of luck, Amy

  • Thanks for this!

    I did notice what appears to be a typo (like you left out the word “not”) in the following sentence: “If you are symptomatic. more herbal or pharmaceutical antibiotics is always the right answer.” Just wanted to mention, in case you want to correct it. (Unless I’m wrong about the typo!)