Bloating Word Cloud


This website is now averaging around 9,000 page views per month, which is frankly amazing to me given how sporadic my blogging has been of late. Of that number, a good 75% are first time visitors so let me say welcome to you all. I realize most of you come here for a post or two and then move on, but it’s gratifying to know that I might have written something that helped you in some way.

In reviewing which posts receive the most views, part eight of my SIBO series is hands down the most popular. There are legions of people out there who suspect they have some sort of gut infection so they apparently come across that article when searching for answers online.

I suppose my experience with garlic is of great interest as well. It’s probably the reason another post of mine, Why Garlic May Be Your Gut’s Best Friend also receives many views.

Today I wanted to revisit treatment options for small intestinal bacterial overgrowth (SIBO) and irritable bowel syndrome (IBS) by writing more comprehensively than I have formerly. Both conditions have the same cause, namely dysbiosis of the gut, but they are considered by medicine to be two distinct conditions only because many who go to a doctor’s office complaining of IBS test negative for SIBO on a breath test.

Obviously, not everyone with IBS has SIBO or SIFBO (small intestinal fungal and bacterial overgrowth). Some may just be reacting negatively to components in their diet.

That said, I do believe standard breath testing misses quite a few people who indeed have an overgrowth of bacteria in the small intestine. Often only hydrogen-producing bacteria are tested for, missing those suffering from an overgrowth of methane-producing species.

Another major limitation of these tests is that they have no way of testing for an overgrowth of yeast in the digestive tract. As I’ve written before, studies where people have undergone an upper endoscopy often find evidence of yeast overgrowth in those complaining of IBS. (1) I suspect that a good number of people who relapse after successful antibiotic treatment do so because an underlying fungal infection has not been dealt with.

Remember that the only thing that keeps native intestinal yeast in check is commensal bacteria. If replenishing beneficial gut flora is not attempted both during and after antibiotic/antifungal treatment, you run the very real risk of never fully resolving your gastrointestinal issues.

OK, time to get to the meat of today’s post.

This article is divided into three sections. The first will discuss which antibiotics have been proven clinically useful for treating either IBS or SIBO. The second will cover the scientific evidence for use of probiotics in these conditions. And the third and final section will review the evidence for natural antimicrobials in the resolution of gastrointestinal complaints.


Several broad-spectrum antibiotics have proven effective for treating bacterial overgrowth and general IBS symptoms. Among them are tetracycline, amoxicillin, clavulanate, metronidazole and flouroquinolones. (2)

Unfortunately, these are all powerful antibiotics that have wide-ranging systemic effects including negative effects on beneficial gut flora. Wipe out those beneficial species and you can end up with serious dysbiosis like a Clostridium difficile infection. According to the Centers for Disease Control and Prevention (CDC), 29,000 people in the United States died of this infection in 2011 alone. Sadly, the death rates haven’t changed much since then.

I would say that the overwhelming majority of those who consult with me do so because of having taken many courses of broad-spectrum antibiotics. While some courses were medically necessary to prevent serious infection or death, others were the result of physicians seemingly ignorant about the long-term health consequences of repeatedly decimating a patient’s beneficial gut flora for the treatment of a medical condition that could have been handled more conservatively.

These broad-spectrum antibiotics, therefore, are rarely recommended to treat gastrointestinal complaints, or at least they shouldn’t be. There are better choices that show minimal impact on beneficial gut flora that a doctor should consider first.

One is neomycin. It is minimally absorbed remaining mainly localized to the gastrointestinal (GI) tract with one exception that I’ll mention shortly. In a randomized, double-blind, placebo-controlled trial examining its usefulness for the treatment of IBS, neomycin resulted in significant reduction of symptoms. (3) Positive outcomes were especially pronounced for those suffering from constipation-dependent IBS. Nor is there much evidence that it negatively affects beneficial gut flora.

But there is a major downside to this antibiotic. Neomycin is considered an ototoxin, meaning it can be toxic to the ear. As such it can lead to hearing loss, loss of balance or both. Bacteria can also build up resistance to it fairly rapidly making it a contributor to antibiotic-resistant bacteria.

A better choice is rifaximin (brand name Xifaxan). It is currently the go-to antibiotic for treating both SIBO and IBS. It’s a synthetic derivative of another antibiotic by the name of rifamycin. It was developed to act locally in the GI tract, and like neomycin it has minimal adverse effects on beneficial gut flora. (4)

This drug is currently available for use in thirty-three countries, although under different brand names. In Canada, it’s known as Zaxine and in India as either Ciboz or Xifapill.

A study published in 2011 in the New England Journal of Medicine reported the results of two identically designed randomized, double-blind, placebo-controlled trials testing its use for two weeks with a ten-week followup in 1,260 patients reporting IBS without constipation. (5)

Those treated with rifaximin consistently achieved relief from IBS symptoms. Many experienced relief from bloating, abdominal pain and improvement in stool consistency. There were no reports of anyone coming down with Clostridium difficile attesting to its minimal impact on beneficial bacteria.

These results confirm an earlier 2006 randomized, double-blind, placebo-controlled study in 124 patients treated for ten days. (6) In that study, those on rifaximin reported significant relief from bloating and flatulence.

There is also evidence derived from lab studies that rifaximin’s potential to cause an increase in antibiotic resistant organisms is low. A study that reviewed charts of previously treated patients found that rifaximin was just as effective the fifth time around as the first. (7)

The effectiveness of rifaximin in treating IBS and SIBO is clinically proven. I certainly would not hesitate taking a prescribed course if the need arose, but would strongly encourage anyone who does so to take a probiotic, including a yeast-based one like Sacchoromyces boulardii, during treatment to help correct the dysbiosis that caused the problem in the first place. I would also advise taking prebiotics to encourage the growth of beneficial bacteria in the colon.


There are a very large number of trials studying the effects of probiotics on various gastrointestinal diseases including IBS. But for the sake of brevity, I’ll be only highlighting three meta-analyses that have examined the issue in-depth. For those who don’t know what a meta-analysis is, it’s an examination of previously published studies meeting certain inclusion criteria that seeks to arrive at an overall consensus concerning the topic under review.

A 2012 meta-analysis examined eighty-four trials that collectively included 10,351 patient participants. (8) These studies variously examined the effects of probiotics on eight gastrointestinal diseases: antibiotic associated diarrhea (AAD), Clostridium difficile disease (CDD), Helicobacter pylori positive (HPP), irritable bowel syndrome (IBS), infectious diarrhea (ID), necrotizing enterocolitis (NEC), traveller’s diarrhea (TD) and pouchitis.

Per the authors of this paper:

“…our meta-analysis containing 74 studies, 84 trials and 10,351 patients shows that in general, probiotics are beneficial in treatment and prevention of GI diseases. The only GI diseases where significant effect sizes were not observed were TD [Traveler’s Diarrhea] and NEC [Necrotizing Enterocolitis]. This effect may be due to the low number of studies on these diseases, or in the TD case, the underlying mechanism of disease, which is often not bacterial. Of the 11 species or species mixtures only L. acidophilus, L. plantarum and B. infantis showed no efficacy, however, for L. acidophilus, it was found that the strain LB was highly effective.”

As for the strains that were most effective the researchers found:

“Eight species yielded significant effect sizes including: VSL #3 which contains viable lyophilized bacteria of four species of Lactobacillus (L. casei, L. plantarum, L. acidophilus, and L. delbrueckii subsp. bulgaricus), three species of Bifidobacterium (B. longum, B.breve, and B. infantis), and one species of Streptococcus salivarius subsp, E. faecium, C. butyricum, L. acidophilus combined with B. infantis, B. lactis, LGG, L. casei, and S. boulardii. The other three probiotic species (L. acidophilus, L. plantarum, and B. infantis), did not show significant efficacy. S. boulardii showed significantly higher efficacy than L. plantarum and B. Infantis. C. butyricum had significantly higher efficacy from the species L. plantarum, L. acidophilus, LGG, L. plantarum and B. Infantis. VSL #3 had significantly higher efficacy than the species S. boulardii, B. infantis, L. plantarum, LGG, B. lactis, and L. acidophilus. As L. acidophilus is one of the most common probiotics we further considered whether differences in efficacy were observed based on particular strains. We found that when analyzed alone, L. acidophilis LB did show significant efficacy…and L. acidophilus with no strain specified did not have a significant effect.”

A 2013 meta-analysis of ten studies examining use of probiotics for the specific treatment of IBS found that taking Bifidobacterium breve, Bifidobacterium longum and Lactobacillus acidophilus reduced pain in IBS sufferers. (9)

Bloating was relieved in those who took B. breve, Bifidobacterium infantis, Lactobacillus casei or Lactobacillus plantarum.

Flatulence was markedly improved in those who took B. breve, B. infantis, L. casei, L. plantarum, B. longum, L. acidophilus, Lactobacillus bulgaricus and Streptococcus salivarius ssp. thermophilus.

The authors of this meta-analysis went on to state:

“In conclusion, evidence suggests that probiotics are an effective treatment option for IBS patients and that the effects of probiotics on each IBS symptom are likely species-specific. Future research should focus more specifically on species, combinations, dose, duration, IBS sub-types, and IBS individual symptoms, while employing standardized measurement tools. Although probiotics are a safe therapy, clinicians should consider other concomitant pathologies when prescribing them to their patients.

Our Research Group in Functional Digestive Disorders and Psychoimmunology, which is within the framework of the Biomedical Research Map of the Aragon Institute of Health Sciences in Spain, is convinced that the key factors in IBS are the immune system and intestinal microbiota after a detailed review of the scientific evidence concerning IBS. Therefore, we think that IBS treatment should focus on both of these factors influencing intestinal dysbiosis by considering the effects of different probiotic species on the symptomatology of individual patients.”

I couldn’t agree more!

The most recent meta-analysis on the use of probiotics for IBS was published on March 14th of this year in the World Journal of Gastroenterology. (10) It reviewed fifteen studies.

This paper found that for abdominal pain, four weeks of probiotics lessened discomfort compared to placebo. However, relief from pain was higher at week eight than at week ten suggesting reduced effectiveness as time went on.

Flatulence and bloating were both improved in adults taking probiotics. This effect was also seen in children afflicted with IBS.

Global IBS scores were also seen to improve after eight weeks of probiotic intake in diarrhea-dependent IBS. Another study analyzed found that four weeks of probiotic intake was effective in reducing IBS symptoms in comparison with placebo.

All three of these meta-analyses are in agreement that taking probiotics improves IBS symptoms and are therefore recommended for this condition. I’ve had several people contact me and report noticeable improvement in their gastrointestinal symptoms after taking probiotics.

Nevertheless, it can be highly beneficial to combine probiotics with a short course of antimicrobial or antifungal agents should a test or symptoms suggest either might be an issue. Those who experience gas and bloating whenever starch and fiber (both soluble and insoluble) are eaten are likely dealing with an overgrowth of bacteria (and possibly yeast) in the small intestine that leads to these substrates being fermented twice: once in the small bowel and again in the colon.

Those who wake up with a tongue coated in yellowish-white gunk or battle stubborn genital and anal itching or suffer from recurring sinus infections may be dealing with an overgrowth of Candida albicans. Those using probiotics with a course of antibiotics and/or antifungals (pharmaceutical or botanical) may have a better chance of preventing a relapse.


My long-time subscribers know that I consider garlic to be the king of antimicrobial and antifungal herbs. I blogged about the research demonstrating these effects here so there’s no need to repeat that information in this post.

Many have written to thank me for sharing my experiences with, and information about, raw garlic because they found it worked effectively for them as well.

The major downside to garlic, of course, is the smell. Sadly, I have yet to come across a garlic supplement that is as effective as raw garlic in treating a GI infection. If you can’t afford to reek of garlic during treatment you need to use something else.

Also remember that the prebiotic fiber in garlic is classified as a FODMAP (fermentable Oligo-, Di- and Mono-saccharides and Polyols). If FODMAPs are the real cause of your IBS symptoms, then raw garlic obviously won’t do you any good if you are not suffering an overgrowth of bacteria or fungi. For more information on FODMAPs please click here and here.

Yet as effective as garlic is, it’s by no means the only botanical to show promise for relieving symptoms related to IBS or SIBO. Quite a few essential oils and extracts have also shown efficacy against gastrointestinal pathogens and symptoms.

In 2013, a paper titled Comparison of the antibacterial activity of essential oils and extracts of medicinal and culinary herbs to investigate potential new treatments for irritable bowel syndrome was published in the BMC Complementary & Alternative Medicine journal. Here are a couple of charts from that paper:



This graph compares the in vitro antibacterial action of three essential oils (coriander, peppermint and spearmint) and three antibiotics (ampicillin, neomycin and rifaximin) against Escherichia coli (E. coli) DH5a with water and methanol acting as controls. Note that all three essential oils were as effective or more effective than rifaximin.


Here’s another chart comparing the antimicrobial action of various essential oils against this same strain of E. coli. Observe the significant effectiveness of pine, tea tree and thyme oil. Coriander seed, lemon balm, lemon grass, mandarin and peppermint also showed antimicrobial activity but at more moderate levels.

The authors of this paper continue on to note that other treatments found effective against IBS contain some of the same oils examined in this paper:

“Mandarin is present in the Chinese herbal medicine Tong Xie Yao Fang (TXYF), and a modified version TXYFa, which has been shown by a systematic review to be potentially effective in the treatment of IBS, since it reduced abdominal pain, distension, flatulence and diarrhoea for up to 6 months after treatment. Absinthe contains fennel (shown in this study and others to have antibacterial properties) as well as wormwood (Artemisia absinthium L.), anise and often lemon balm, Roman wormwood (Artemisia pontica L.) and hyssop (Hyssopus officinalis L.). Although absinthe is now thought of as an alcoholic beverage, with unhappy connotations due to its ability to cause absinthism when drunk to excess, it was originally used in the 1780s to cure colic (aka IBS) and fight dysentery, which would correlate with its probable antibacterial activity.”

N-Acetyl Cysteine

N-acetyl cysteine (NAC) is a precursor to glutathione, the body’s master antioxidant. But it is also extremely effective at piercing the slimy extracellular matrix of bacterial biofilms, something most antibiotics are incapable of doing on their own. (11)

Therefore, I highly recommend anyone suffering from any digestive disorders, including IBS, to begin taking 600 mg of NAC twice daily, especially if they are taking a synthetic or natural antibiotic. I personally recommend Jarrow Brand NAC.

However, please don’t start this regimen until you have ready access to a toilet throughout the day as taking NAC at these levels can lead to a rapid die-off with a resultant urge to defecate. Also, you may come down with what is known as NAC flu, which is characterized by aching joints, lethargy and headache. This too is due to die-off.

This regimen, therefore, is best done when you have some time free from work. I also advise drinking plenty of water and refraining from any alcohol consumption as your liver will be very busy detoxifying. Two to three days at this level of intake should be sufficient, after which you may want to take 600mg daily as a prophylactic.


It should be apparent that there are many ways to treat IBS or an overgrowth of pathogens in the small intestine. But please don’t lose sight of the fact that antibiotics and antifungals are just part of the solution.

At the end of the day, you have to figure out a way to prevent gut dysbiosis from rearing its ugly head after an infection has been resolved. That often involves changes to diet as I’ve outlined in numerous posts sprinkled throughout this blog. It may also mean avoiding certain medications like proton pump inhibitors and other acid-suppressing drugs or opioid analgesics.

Remember, you need to nurture the beneficial gut bacteria that keep the ecology of your intestinal tract diverse and healthy. If you haven’t read my post Internal and External Ecosystems, please do so. It explains why what is missing from your digestive tract is often more important than what is plaguing it.





4 Thoughts on “IBS Treatment Options

  1. David on 11/06/2015 at 12:09 am said:

    This seems like a good summary of the options, but surely it depends on which species are overgrowing? As I understand it, most overgrowth is likely to be bifidobacteria, but there could be other bacteria involved, and would the antibiotics you mention be effective against them?

    For example, it was suggested in a Facebook group that while C Difficile normally acts in the large intestine, it is possible for it to lodge in the small intestine and overgrow there, making it very difficult to eradicate.

    And as you say, yeasts will not be susceptible to the antibiotics either. What this suggests to me is that for effective treatment, it is desirable to first identify which organisms are the problem via whatever tests are available. Maybe stool analysis might help, or Organic Acid Tests?

    The same probably applies to probiotics – you do not want to be pushing more of the species causing the problem into an already overloaded situation. I suspect I did that to myself recently 🙁

    Digressing slightly, I have read that yeasts and heavy metals are closely related. Yeasts are one of the mechanisms that the body uses to eliminate heavy metals via the digestive system. The suggestion is that you have a lot of heavy metals to get rid of, yeast will appear to do this – cause and effect! Then the question is whether you should try to remove the yeast, because that will leave the heavy metals floating around in the body where they will be reabsorbed. Once the heavy metals are gone, the yeast will return to more normal levels.

  2. rjmedina on 11/06/2015 at 9:30 am said:

    Hi David.

    Thanks for commenting.

    No one knows exactly what inhabits our guts, let alone what species and yeasts may overgrow in either the small or large intestine. The problem is that many of these organisms do not survive outside of the body so can’t be cultured. We can look for genetic markers, of course, but that still leaves an awful lot of questions unanswered.

    What we do know, at least in relation to IBS and SIBO, is that an antibiotic like rifaximin is effective in relieving symptoms and for many that’s all they desire. I know that when I was afflicted with my GI problems, I was desperate for anything that would just make it go away so I could get my life back.

    The tests you mention may indeed help, so I don’t discount their use out of hand. But even having this information can still make it vexing to correct gut dysbiosis. There are so many factors that can disrupt gut flora, including mental stress, that it really requires a holistic approach to solve.

    The hypothesis on yeast and heavy metals is an interesting one. It could also be the case that heavy metals so disrupt beneficial gut flora that it gives yeast an opportunity to fill those now vacated niches.

    I’ve always suspected that our native yeast are there for a reason. We, of course, only notice them when they get out of hand. But I suspect they, like many potential pathogens like C. diff or E. coli, play a beneficial role when part of a diverse and healthy gut ecosystem.

  3. David on 11/06/2015 at 3:24 pm said:

    The gut is a very complicated system where everything plays a part. My gut has been bad since I was a baby, and I can trace the consequences of that my whole life. Earlier this year, I did a stool analysis which showed a variety of interesting things: no bifidobacteria at all, overgrowth of clostridium and strep, low lactobacillus, high commensals. In trying to increase the bifidobacteria, I took it orally which I think caused or aggravated my SIBO. It makes me wonder whether many cases of SIBO are caused/aggravated by attempts to fix gut problems.

    I was intrigued with your Facebook share recently about Robogut, where they make artificial stool from about 28 bacterial strains and insert it by colonoscopy. This would be a way of avoiding the small intestine. The first thing I wondered was whether 28 was enough to restore a “normal” mix to the large intestine, given that normally there are hundreds. The second thing was why they needed a machine to mix it up. I read a story recently of a fellow who cured ulcerative colitis by giving himself probiotic enemas with a random mix of ordinary probiotics every 2-3 days for a couple of months. Maybe bypassing the small intestine is a good way to avoid SIBO?

  4. rjmedina on 11/06/2015 at 3:58 pm said:

    Fecal transplants are being shown quite effective at curing C. diff infections and I really hope they catch on to avoid the unnecessary deaths caused by this horrible type of dysbiosis.

    I don’t think there will ever be a therapy that can completely recreate the thousands of species in a digestive tract. Research seems to suggest that this isn’t really necessary. It’s appears that just introducing key bacterial species is enough to make the gut environment hospitable to other beneficial inhabitants while simultaneously making it inhospitable to pathogen replication.

    Yes, there are successful cases of people curing serious intestinal diseases by self-administering enemas, both with fecal and probiotic matter. I just don’t see health authorities ever encouraging do-it-yourself fecal transplants, however, because of the risk of unwittingly catching some nasty diseases like HIV or hepatitis if the donor is a carrier of either.

    There are several good ways to avoid SIBO. One is by not inhibiting gut motility. The migrating motor complex is key to maintaining a healthy small intestine. Another is not suppressing stomach acid. A third is to avoid immune suppression. A fourth is to avoid excess alcohol intake. Another major cause is food poisoning so being careful what you eat and how it’s prepared is also important. Speaking to this later point, I imagine that some of the unfortunate victims of the recent Chipolte food poisoning outbreak will end up battling SIBO.

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