Small Intestine Bacterial Overgrowth is a hot topic in the functional medicine world.  SIBO can be defined as an increase in the number or the type of bacteria in the small intestine leading to many unpleasant GI symptoms like bloating, abdominal pain, constipation and diarrhea [i] Opinions on how to effectively treat SIBO seem to differ widely among practitioners. When I was diagnosed with a mild case of SIBO, I dove head first into the online SIBO communities and the functional health blogosphere to unearth the best strategies to eradicate the unwelcomed visitors in my small intestine. But, instead of clarity, my research into the matter yielded utter confusion. Many leaders in the field seemed to endorse radically different SIBO protocols; which created heated and polarizing debates in the online communities. Amidst this SIBO universe fray, the contestation around probiotic use during treatment seemed especially volcanic.

The probiotic haters believe that probiotics during SIBO treatment will only add fuel to the fire (or bacteria to the overgrowth). They believe that a damaged Migrating Motor Complex inhibits the patient’s ability to successfully move the bacteria to the large intestine. The Migrating Motor Complex (MMC) stimulates the wave like contractions within the GI tract that cleanses your digestive system to prepare for its next meal.[ii] A break down in the MMC decreases motility allowing bacteria and food to sit in the small intestine leading to fermentation and the development of SIBO.[iii]  You can think of the MMC like a broom that sweeps the small bowel clean after a meal. The anti-probiotic camp believes that even when the overgrowth in the small bowel is cleared with antibiotics that a compromised MMC will likely cause relapse in patients. The probiotic advocates seem to present the argument that SIBO is usually rooted in dysbiosis (an imbalance of bacteria) within the large intestine. They believe that recurrence of SIBO is eminent if large intestine dysbiosis is not addressed. These practitioners tend to use probiotics in conjunction with herbal or natural antibiotics (usually prescribing a round of probiotics following their antibiotic regiment). When trying to figure out whether to use a probiotic during my own treatment, I often felt torn between the two arguments. And nothing is worse than uncertainty when treating a medical problem as unpleasant as SIBO. Luckily, a little research led me to a clearer understanding of probiotics and their impact on SIBO treatment. I’m hoping that this blog can help some other confused sufferers come to a better understanding as well! Lets dig into it!


What does the research say?

The research on probiotics and SIBO is still in its infancy, but there have been some interesting studies directly looking at treatment of SIBO with probiotics.  Most of the current research seems to show positive outcomes from probiotic use during SIBO treatment. A pilot study aimed at exploring the efficacy of probiotics in SIBO treatment analyzed a group of thirty people who had positive hydrogen breath tests.[iv] The researchers split the participants into two groups, an experimental group and a control group. Both groups received a three-week regiment of broad spectrum antibiotics followed by a fifteen-day maintenance antibiotic therapy. During the maintenance antibiotic therapy, the experimental group took a probiotic supplement containing Bacillus coagulants  and the control group took the antibiotic alone. Six months after the study, 93% of the probiotic group had a negative breath test compared to only 67% of the control group. In addition, 100% of the probiotic group compared to only 47% of the control group reported being pain free. Bloating, belching and diarrhea also were much lower in the probiotic group versus the control group. Although the study was small, the probiotic group showed better long-term outcomes. The probiotic advocates might even argue that the probiotic could have corrected the underlying imbalance in the large intestine leading to more negative breath tests and better symptom outcomes in the experimental group.


There have also been a number of studies that have shown positive outcomes with probiotic treatment alone for SIBO treatment:

  • A small pilot study compared the effectiveness of a five-day treatment of probiotics versus an antibiotic (Flagyl), which resulted in 82% of the probiotic group reporting symptom improvement after the study compared to only 52% of the antibiotic group fifteen days post treatment.[v] The strains used in this study were Lactobacillus casei, Lactobacillus plantarum, Streptococcus faecalis and Bifidobacterium brevis. It is also important to note that both groups were also on a diet that limited legumes, alcohol, leafy greens and dairy.
  • Another small pilot study treated SIBO patients with a six-week course of the probiotic strain Lactobacillus casei. This resulted in a negative breath test in 64% of the participants.[vi]
  • Forty SIBO sufferers with an abnormal glucose breath test were given two billion spores of Bacillus clausii three times a day for one month.[vii] 47% of the participants produced a negative breath test with only one patient experiencing side effects (constipation). 47% may not seem super high, but it is a comparable normalization to some broad-spectrum antibiotic treatments for SIBO.

It is also important to note that other than the Flagyl vs. probiotic study, all the research was conducted without diet or lifestyle changes during the experimental period. Normalization of breath test would have probably been higher if participants had adopted a more primal diet during treatment. Also, it would be interesting to see if a study that used herbal antibiotics in conjunction with probiotics would produce an even higher rate of breath test normalization.

In general, the literature is pretty sparse when it comes to direct research involving SIBO and probiotics. There is a wider body of research involving treatment of IBS with probiotics that could provide some meaningful insights since research has shown between 75-84% of people with IBS have SIBO. [viii][ix] In a recent meta-analysis that reviewed data from 9 different clinical trials, the researchers concluded that: “probiotics reduce pain and symptom severity scores. The results demonstrate the beneficial effects of probiotics in IBS patients in comparison with placebo.”[x] When looking at the various studies within this meta-analysis, it seemed that probiotics either significantly reduced IBS symptoms or they produced no change in symptoms. Adverse effects were rare in these studies. Leaving me to believe that it is safe and usually beneficial for someone with IBS, and by association probably SIBO as well, to try probiotics. All of the available research on the matter seems to suggest that while there is no guarantee of effectiveness necessarily, there isn’t anything to suggest harm in giving them the old college try.


Why might probiotics be helpful in SIBO treatment?

Based on the limited evidence we have reviewed so far, it seems like there is more evidence backing the probiotic camp, but I think it is important to take a closer look at the anti-probiotic argument. This camp argues that the disturbed MMC in SIBO patients will inhibit the person’s ability to clear the probiotics from the small intestine leading to an even bigger overgrowth. Although there is research that proves SIBO positive people have delayed motility, I was unable to find research that supported the argument that probiotics delay motility further. There are, however, some interesting studies on rats showing that the colon’s bacteria play an integral role in a healthy MMC response.[xi] The researchers recorded MMC activity of rats that were manipulated to be “germ free” (without any gut bacteria). The researchers then inoculated the same rats with gut flora from other rats and recorded MMC activity again 7-10 days later. The MMC intervals decreased by 56% after the rats had been inoculated, a process, which was associated with faster transit through the small bowel. In other words, once the rats had a healthy population of gut bugs, the broom like action of the MMC increased the number of sweeps resulting in increased motility. In a follow up study, the same researchers found that certain strains of bacteria affect the cleansing waves of the MMC.[xii] Lactobacillus acidophilus and Bifidobacterium bifidum strengthened the MMC response and increased transit while E Coli and Micrococcus luteus inhibited the MMC resulting in delayed small intestine transit.9 These studies indicate the importance of colonic micro biota in producing a healthy and functioning small bowel. Considering these findings, it seems illogical to think that you could treat SIBO without addressing the gut imbalances in the large intestine. Probiotics serving as powerful vehicles to re-establish the balance in the large intestine seems to be crucial to the eventual restoring of proper function in the small intestine.

Probiotics help establish a healthy balance through three main mechanisms.  First, probiotics have been shown to play a powerful role in modulating the guts immune system.[xiii] There is a high prevalence of SIBO in individuals that have immune-compromised conditions making the immune modulating effects of probiotics valuable in treatment.[xiv]   Second, probiotics produce anti-microbial compounds that can help eliminate pathogens.[xv] These antibiotic compounds can attack the overgrowth in the small intestine head on. Probiotics also produce enzymes that contribute to the production of short chain fatty acids that reduce the pH of the lumen creating an unfriendly environment for pathogenic bacteria.xv Third, probiotics strengthen the guts mucosal barrier and inhibiting adherence of pathologic bacteria to the walls of the GI tract.xv


Why might some people react negatively to probiotics?

Based on the research, I am led to believe that there is no harm in giving probiotics a try if you have SIBO. Does that mean everybody with SIBO is going to benefit from probiotics? Absolutely, not. Treating SIBO is complex and every case is different. Probiotics might be very effective for one person and not effective in another. But, I don’t think you should be afraid to try them. Also working with a functional practitioner would help you to determine the right timing and probiotic that is most appropriate for your individual case. Here are some other important things to consider when choosing a probiotic:

  • Bacterial strains used. The bacterial strains have different effects. Chris Kresser has stated that many of his patients with histamine issues react negatively to lacto-based probiotics. But, he has also said that many of his SIBO patients do well with spore-based probiotics like Prescript Assist. I have also seen countless positive reports on the SIBO Facebook group about the effectiveness of MegaSporeBiotic; which like Prescript Assist is a spore based probiotic.
  • Source of bacteria. People with histamine issues seem to have problems with fermented foods and would most likely tolerate a supplement better.
  • The prebiotic content of different probiotics. Some individuals might react negatively to the prebiotics that are often found in probiotic supplements such as FOS. In that case, you could try a probiotic that doesn’t contain any prebiotics. If you find that you can’t tolerate any probiotics, then you may benefit from focusing on repairing your MMC and reintroducing probiotics later.
  • Timing. In the defense of the anti-probiotic argument, some people don’t tolerate probiotics at the beginning of treatment due too severely compromised gut motility. But, I don’t agree with the argument that they should avoid probiotics forever considering their impact on bacterial balance in the large intestine. These patients may tolerate probiotics much better after antibiotic treatment. However if they still are having issues, then it might be best for them to focus on repairing the MMC and reintroducing probiotics later. Exercises to stimulate your Vagus Nerve like gargling and humming can help strengthen your MMC response.[xvi] Prokinetic supplements such as Iberogast and Motilpro that help stimulate motility may also be helpful.


Bottom Line: Research has shown positive outcomes with the use of probiotics in SIBO treatment. Probiotics are essential in restoring healthy balance of good bacteria in the colon that which is necessary for healthy small intestine function. Working with a functional practitioner to determine the proper strains, the right sources and the optimal timing of probiotic implementation will increase the effectiveness of treatment.


[i] Bures J, Cyrany J, Kohoutova D, et al. Small intestinal bacterial overgrowth syndrome. World Journal of Gastroenterology : WJG. 2010;16(24):2978-2990. doi:10.3748/wjg.v16.i24.2978.

[ii]Telford GL, Sarna SK. The migrating myoelectric complex of the small intestine. Chaos. 1991 Oct; 1(3):299-302

[iii] Miyano Y, Sakata I, Kuroda K, et al. The Role of the Vagus Nerve in the Migrating Motor Complex and Ghrelin- and Motilin-Induced Gastric Contraction in Suncus. Covasa M, ed. PLoS ONE. 2013;8(5):e64777. doi:10.1371/journal.pone.0064777.

[iv] Khalighi AR, Khalighi MR, Behdani R, et al. Evaluating the efficacy of probiotic on treatment in patients with small intestinal bacterial overgrowth (SIBO) – A pilot study. The Indian Journal of Medical Research. 2014;140(5):604-608.

[v] Soifer LO, Peralta D, Dima G,Besasso H. Comparative clinical efficacy of a probiotic vs. an antibiotic in the treatment of patients withintestinal bacterial overgrowth and chronic abdominal functional distension: a pilot study. Acta Gastroenterol Latinoam. 2010 Dec;40(4):323-7

[vi] Barrett JS, Canale KE, Gearry RB, Irving PM, Gibson PR. Probiotic effects on intestinal fermentation patterns in patients with irritable bowel syndrome. World Journal of Gastroenterology : WJG. 2008;14(32):5020-5024. doi:10.3748/wjg.14.5020.

[vii] Gabrielli M, Lauritano EC, Scarpellini E, Lupascu A et al. Bacillus clausii as a treatment for small intestine bacterial overgrowth. The American Journal of Gastroenterology. 2009: 104:1327-1328. doi:10.1038/ajg.2009.68

[viii] Pimentel M, Chow EJ, Lin HC. Normalization of lactulose breath testing correlates with symptom improvement in irritable bowel syndrome: a double blind, randomized controlled study.  Am J Gastroenterol.2003;98:412-419.

[ix] Nucera C, Lupascu AM, Gabrielli M.  et al.  Sugar intolerance in irritable bowel syndrome: the role of small bowel bacterial overgrowth.  Gastroenterology.2004;126(4[suppl 2]):A511.

[x] Didari T, Mozaffari S, Nikfar S, Abdollahi M. Effectiveness of probiotics in irritable bowel syndrome: Updated systematic review with meta-analysis. World Journal of Gastroenterology : WJG. 2015;21(10):3072-3084. doi:10.3748/wjg.v21.i10.3072.

[xi] Husebye E, Hellstrom PM, Midtvedt T. Intestinal microflora stimulates myoelectric activity of rat small intestine by promoting cyclic initiation and aboral propagation of migrating myoelectric complex. Dig Dis Sci. 1994 May;39(5):946-56.

[xii] Husebye E, Hellstrom PM, Sundler F et al. Influence of microbial species on small intestinal myoelectric activity and transit in germ-free rats. Am J Physiol Gastrointest Liver Physiol. 2001 Mar;280(3):G368-80.

[xiii] Plaza-Diaz J, Gomez-Llorente C, Fontana L, Gil A. Modulation of immunity and inflammatory gene expression in the gut, in inflammatory diseases of the gut and in the liver by probiotics. World Journal of Gastroenterology : WJG. 2014;20(42):15632-15649. doi:10.3748/wjg.v20.i42.15632.

[xiv] Grace E, Shaw C, Whelan K et al. Review article: small intestinal bacterial overgrowth – prevalence, clinical features, current and developing diagnostic tests, and treatment. Alimentary Pharmacology and Therapeutics. 2013:38(7):674-688

[xv] Patel R, DuPont HL. New Approaches for Bacteriotherapy: Prebiotics, New Generation of Probiotics, and Synbiotics. Clinical Infectious Diseases. 2015: 60(2): S108-S121

[xvi] Vaccination Infoormation Network. Gut Brain Access and its role in Disease. 2014. Video File.


  • Great blog post! I have had success with Bifido Maxiums from the Gut Institute. It caused die off for a couple of weeks. Thanks for putting the time in to write this.

  • Thanks for the info. I have been using them for 2 weeks. Sadly, I don’t think they are affecting me in any noticeable way. At least they didn’t cause a flare up.

    • I know that the MegaSpore people say that for some people it takes like 3 months on the therapeutic dose to really feel a large impact. I noticed a big difference once I completed my first bottle. Keep me posted!

  • Great article! Unfortunately you can only order Megasporebiotic if you’re a doctor 🙁 and I live 2 hours away from the nearest provider of the probiotic. Any suggestions?

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  • If u got the anti vinculin antibodies. U have a damaged mmc for life. Even if u take probiotics that stimulate the mmc, it does do more harm then good because they just get stuck in small intestine because there is lack of motility. And these good bacteria ferment and cause gas too. The problem is having antibodies in the blood that attacks the motility nervs called vinculin. In those people like me… taking mmc promoting probiotics cause even a sibo relapse. After rifaximin I was sibo free for months. Almost a year. Sibo didnt come back while doing low fodmap diet. Then i started an mmc improving probiotic and i did relapse sibo after 10 days. It was terrible!! The diffrence is…. there are a lot of people calling they have sibo. But actually research shows now that it isnt sibo for those who can take probiotics and improve. They actually have a bloom in large intestine and dont have much lack of motility in small intestine. They got lack of motility in large intestine only because of the archae and methane bacteria. So these people take probiotics and sure it makes them better as they dont get stuck in small intestine. People with vinculin antibodies have the real sibo type wich is the worst. They have no mmc in small intestine. Thats why every probiotic makes them worse and even relapses them. I dont know one person with vinculin antibodies that did improve on probiotics. There is a big diffrence in motility in small and large intestine. If u dont have motility in small intestine. Probiotics will never, never work.

    • Hi KK! Thanks so much for your comment and perspective! I know that vinculin antibodies is definitely a sub group of people with SIBO! You are right to speculate that people with vinculin antibodies may have a compromised MMC for life. But, vinculin antibodies should diminish over time (in most cases) post infection. As the antibodies diminish, there is still an opportunity for the MMC and nerves to regenerate once vinculin antibodies diminish. The amount of time for these antibodies to subside is going to vary from person to person. You are so right in saying that maybe people with high antibody levels may be better off skipping probiotics. But, once the antibodies lower….probiotics may be helpful. I definitely think MMC repair or support (if nerve damage is so bad) is essential for SIBO recovery/treatment. In order for the MMC to function properly, there needs to be healthy bacteria in the large intestine. Therefore, probiotics can be helpful in restoring the MMC. Vagus Nerve exercises are also a must!! But, antibody levels may be a good indicator to determine if probiotics are appropriate at a particular time during treatment. Thanks again for sharing!