Leaping for joy because his SIBO is gone!

This is the eighth and last installment of the Gut Critters series on small intestinal bacterial overgrowth (SIBO). In this post, I want to talk about treatment options for SIBO.


Assuming you test positive for SIBO what’s next? Well, the standard course of medical treatment involves antibiotics. The problem for the physician, however, is determining which antibiotic to choose.

What works against one type of pathogen may not work against another. And since it’s rarely just one type of pathogen causing SIBO, the options can get complicated. Throw in yeast issues and the treatment conundrum gets worse. For this reason, there is no common agreement about the choice, the dosage or how long to prescribe a course of antibiotics. A perfect illustration that medicine is as much art as science.

Long-term, broad-spectrum antibiotic use is not an ideal choice as they are more likely to cause a growth of pathogenic bacteria like Clostridium difficile, a blooming of Candida albicans and potentially lead to the growth of antibiotic-resistant bacteria in the patient.

Tetracycline was the treatment of choice for a long time but in one clinical trial, only 3 out of 11 subjects experienced a normalization in their breath tests after their course was finished. Granted, this is a very small trial, but so are most of the studies examining SIBO treatments.

Other antibiotics that have shown promise include amoxicillin-clavulanic acid, ciproflaxacin, chloramphenicol, doxycycline, metronidazole, neomycin, norfloaxin, trimethroprim-sulfamethoazole and rifaximin.

Of these, rifaximin (brand name Xifaxan) has shown the most promise in clinical trials for treating SIBO in irritable bowel syndrome (IBS) sufferers. It’s a semi-synthetic antibiotic that is usually given for 7 to 10 days. Depending on the clinical trial referenced, symptoms improve for 33% to 92% of participants taking it and rifaximin completely eradicates overgrowth in 80% of infections.

As with any drug, there are side effects involved with taking an antibiotic which I’ve covered in a previous post. So I recommend that you supplement with a good probiotic and prebiotic while on them.

As I mentioned in the first post in this series, yeast overgrowth is likely also part of SIBO. Not for everyone, but for a sizeable number. When beneficial gut flora populations are disordered, not only is there an overgrowth of pathogenic bacteria, it’s also usual for resident yeast populations to overgrow as well.

If you have genital yeast issues (vaginal yeast in woman, jock itch in men) or a white coating on your tongue (thrush), alert your doctor so that an appropriate anti-fungal is made part of your treatment protocol.

Probiotics and Prebiotics

SIBO is impossible without disruption to our beneficial gut flora; disruptions caused by many things like licit and illicit drug use, binge drinking, stress, diet, viral and bacterial infections, etc.

So the interest in using probiotics and prebiotics for treating SIBO is growing but is it scientifically valid?

In the case of prebiotics, scientific evidence for its beneficial use is scanty at best. There currently are no large randomized controlled trials in the literature to answer this question but hopefully this will soon change.

As you may recall from my post on prebiotics, I consider them fertilizer for gut flora in the colon. By feeding your friendly colonic bacteria, they grow and outcompete other colonic pathogens. However, the main locus of action for prebiotics is in the colon, not the small intestine.

Nevertheless, many cases of SIBO are due to gram-negative bacteria migrating from the colon. So I can see a definite benefit in encouraging the growth of bifidobacteria to control the spread of these pathogens. But whether encouraging these colonic species can help correct an existing case of SIBO is still unresolved.

The issue with any fiber, however, is that when suffering from SIBO this fiber will be fermented twice: once in the small intestine and again when it reaches the colon. This often leads to lots of gas and bloating which can be quite uncomfortable.

It’s for this reason that prebiotic fiber is discouraged on the FODMAP elimination diet in the treatment of IBS. However, as I pointed out here, there is a downside to doing so namely the failure to feed beneficial gut flora.

There is evidence to suggest that antibiotics, whether natural or synthetic, are more effective when prebiotic fiber is present because it causes these pathogens to “wake up” when fed making them more susceptible to being killed. As you’ll soon read in regards to crushed garlic, this may be another reason this herb is so effective.

The research on probiotics for the treatment of SIBO is more promising. I’ve covered many of the functions of beneficial bacteria here but let me quickly recap.

As in the colon, beneficial bacteria outcompete pathogens for both food and attachment sites. Unlike the colon, however, the predominant species in the small intestine is Lactobacillus.

Lactobacillus strains, like Bifidobacterium, produce lactic acid to make the small intestine inhospitable to pathogens. They also produce antimicrobials that directly target harmful bacteria. They strengthen the gut’s immune response to infection by communicating with the structures that form the gut-associated lymphoid tissue or GALT system. They strengthen the gut wall preventing translocation of pathogens to systemic circulation. They exert a strong anti-inflammatory effect along the gut wall. And since they regulate the growth cycle of the absorptive cells that line the small intestine, they are absolutely essential to digestive health and your eventual recovery through diet.

This doesn’t exhaust all their vital function, but it’s enough for the purposes of this post.

In one small randomized clinical trial among 12 patients, administering Lactobacillus casei and Lactobacillus acidophilus proved effective against bacterial overgrowth that resulted in chronic diarrhea. However, Lactobacillus fermentum proved ineffective. Just like antibiotics, probiotic strains differ in their actions against harmful bacteria.

No form of gut dysbiosis can be cured without introducing beneficial probiotic strains into your digestive tract. How you do that is up to you.

Some focus on eating fermented foods like yogurt or kefir. Unfortunately, many of these foods are also high in histamine which can be a problem for some people. Others avoid eating any dairy making this choice unfeasible. The other option is to take a daily probiotic.


As many of you already know, I was never officially diagnosed with SIBO, “just” irritable bowel syndrome. My doctors—yes there was more than one—ordered many tests that led to my diagnoses of IBS but no one ever thought to test me for SIBO. I certainly had never heard of SIBO so I didn’t know to ask. As mentioned, not being screened for SIBO when diagnosed with IBS is all too common in this country.

So with nothing but a newly minted IBS diagnosis to my name, I began my search for answers, first online and afterwards at the local university science library. It was then that I discovered I had all the classic signs of someone suffering from a small intestinal bacterial overgrowth.

I considered calling my physician and requesting a referral to a gastroenterologist for a hydrogen breath test, but by this point I was so tired and discouraged with the medical system, I decided to try garlic instead.

Why garlic? Because of its well-known antibacterial, antiviral, antifungal and antiparasitic properties. I figured if I did have SIBO and a yeast overgrowth why not give it a shot? If it didn’t work, I could always make the request to see a gastroenterologist.



Let me be crystal clear and say this is what I felt was right for me at the time, not what I’m recommending to anyone reading this blog. As the disclaimer statement to the right reads, I’m not a medical doctor nor do I play one on the internet.

I also didn’t attempt this until after I had been given a series of tests by my doctor(s) that ruled out a lot of other conditions, including parasites. It was only after they told me that I had IBS, but was given no other advice other than to watch my stress levels and eat plenty of fiber (?!?!?), that I embarked on this experiment.

So what follows is my experience using raw-organic garlic to treat my IBS and what I believe was SIBO and yeast overgrowth.

During the first week, I took a garlic supplement but apart from some bad breath, I didn’t notice anything different other than that my wallet was lighter than before. So I decided to try the real deal. Another benefit of raw garlic is that it has inulin, and I figured it would at least feed my bifidobacteria if nothing else.

I had read that imported garlic was irradiated by the USDA at the border. Unfortunately, irradiation kills the enzyme allinase and it’s this enzyme that is responsible for forming the active ingredient allicin when a clove of garlic is crushed or chopped. So I was careful to use only organic garlic that I sourced from a local health-food store or farmer’s market.

I knew I had to eat it raw to derive any benefit but wasn’t looking forward to it. I love garlic but eating it raw can be a bit much, but unfortunately, there was no way around this. I used a garlic press to crush one to two cloves into a glass, added fizzy water to make the garlic bits float to the top and waited a minimum of 15 minutes before drinking to allow the allicin time to form.

Please note that a clove is one small piece of a garlic bulb. I once told this story to someone who will remain anonymous, and they went home and tried to eat a whole bulb of garlic instead. Mother of God! Are you crazy I exclaimed? I’m shocked they could get most of it down without vomiting!

I soon learned it was best to take this garlic “juice” on a full stomach or risk nausea. I did this after each meal, including breakfast, if you can imagine, for about seven days. So what happened?

Well, at first I felt a lot of stomach discomfort and rumbling. Then the need to go to the bathroom became overwhelming. It was not unusual to experience cramping as well. And what showed up in the toilet was like nothing I had ever seen before or since. I can only describe it as fudge-like in consistency with a very reddish-brown hue. I’ll leave it at that.

This went on for several days until my stools returned to normal. By then all of my IBS symptoms disappeared. I was shocked to say the least as nothing else had worked until then. What the garlic killed is still a mystery to me. Was it bacterial or fungal or both? I don’t know or really care. I was just happy it, whatever “it” was, was finally gone. I have not seen a doctor for anything other than a physical in the last two years.

Nevertheless, there were some definite unpleasant side effects.

The lingering garlic taste in my mouth and strong garlic body odor was a big issue. I noticed people giving me a wide berth when they approached me. Heck, even my dog was less likely to get near me, and she can’t stand being alone! On the plus side there wasn’t a chance in hell a flea or vampire was going to suck my blood during this garlic fest.

As with any herbal medicine, there’s no way of knowing how much of the active ingredient you’re actually getting. I noticed that my reaction would vary with cloves from different bulbs. Some bulbs would be stronger than others. No doubt this is due to differences in how they were grown and the time since harvest. Unlike a prescription drug, there is just no way to control for this.

As mentioned there was stomach upset, cramping and unpredictable visits to the bathroom. Lucky for me, I work out of my home, but if I didn’t, I don’t think I would have chanced it, at least not during the work week.

The amount of inulin in garlic is also unpredictable so at times gas produced in the colon due to fermentation was made worse.

I also learned to not take it anywhere near bedtime or the rumbling/cramping/bathroom dashing would keep me up for part of the night.

So that, dear reader, was my experience with taking garlic for my IBS. As I said, I’m not recommending you try this only that it was the treatment option that worked for me.

(I’ve since posted a more comprehensive article about garlic here)


Once a case of SIBO is successfully treated, how permanent is the treatment?

Sorry to say the figures aren’t encouraging as relapse rates are high. In one study that followed 80 patients prescribed rifaximan, 35 people or 44% had a recurrence of SIBO within nine months after successful treatment. God only knows how many had a recurrence after nine months.

These figures are even worse if you’re older, have had an appendectomy, have short-bowel syndrome or continue taking proton-pump inhibitors. No doubt diet plays a huge factor in relapse so if you haven’t read my posts on dietary causes predisposing to SIBO please do so.

Final Words

Those who’ve suffered with IBS or SIBO know it’s no walk in the park. Whether you stay free of SIBO once cured will largely come down to staying away from those factors that impair gastric barrier function, slow intestinal peristalsis and harm your beneficial gut flora. Not all of these factors are within your control. Previous surgical operations, radiation therapy, AIDS and cystic fibrosis are just some examples of this.

Nevertheless, many of the predisposing factors I’ve outlined in this series are within your control. I credit changes to my diet and staying away from these non-dietary causes for remaining IBS free for over two years. I hope sharing my experience and knowledge with you leads you to the same place.

To your health!


A more up-to-date post on IBS and SIBO treatment options can be found here.



Bergner, P. (1996). The Healing Power of Garlic. USA: Prima Health.

Bures J., Cyrany J., Kohoutova D., et al. (2010) Small intestinal bacterial overgrowth syndrome. World Journal of Gastroenterology, 16(24): 2978-90.

Quigley E. M. M., Quera R. (2006). Small Intestinal Bacterial Overgrowth: Roles of Antibiotics, Prebiotics and Probiotics. Gastroenterology, 130: S78-S90.

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