SIBO: How Small Intestinal Bacterial Overgrowth Impacts Your Microbiome & Your Overall Health

SIBO: How Small Intestinal Bacterial Overgrowth Impacts Your Microbiome & Your Overall Health

  • Gut Health

  • By Desiree Nielsen, Registered Dietitian

    As our awareness and interest in the gut microbiome grows, it is no longer a surprise to hear about the trillions of bacteria living in your digestive tract. However, it may surprise you to learn that such bacterial abundance should be confined mainly to the dark recesses of your colon. By the time your digestive contents reach your colon, roughly 80-95% of all of your nutrients have been digested and absorbed. This lack of nutrition, coupled with the work of your immune system, keeps your bacteria in check and helps to moderate their growth.

    Your small intestine, on the other hand, is not meant to be microbe-rich. In fact, there is a valve between your small intestine and colon known as the ileocecal valve that helps ensure that the contents of your colon – including the bacteria there – don’t travel backwards. Compared to the trillion or so bacteria per millilitre in the colon, there may be as few as a hundred bacteria per millilitre in the early part of the small intestine, the duodenum1. This makes sense for a couple of reasons; the duodenum receives acidic contents from the stomach and neutralizes them with very alkaline secretions; the dramatic shift in pH makes it difficult for microbes to survive1. In addition, this part of your gut is awash in a nutrient flood multiple times a day. If there are a lot of bacteria living there, it would be akin to serving them a lavish buffet…and no one likes leaving a buffet early.


    Defining SIBO

    Should a larger bacterial population get established in the small intestine, it’s known as small intestinal bacterial overgrowth or SIBO. SIBO has been a popular topic in integrative and naturopathic circles for some time; however, there is still a degree of discomfort with it in conventional medical circles. Understandably, one of the reasons for this is the lack of clear, specific diagnostic methods2,3.

    The best diagnostic available is a direct sampling of the contents of the small intestine2,3. It is generally agreed that SIBO is present when bacteria surpass 100,000 CFU per ml but even numbers beyond 1000 CFU per ml may be sufficient2,3,5. Typically, these bacteria will be of the gram-negative type more common in the colon, as opposed to the gram-positive type more typical in the small intestine. However, this type testing is invasive and not a first resort for most. In addition, even direct sampling cannot provide a complete assessment of a bacterial community that has plenty of members hiding out deep in the folds of the small intestine.

    A less invasive (and more commonly practiced) strategy is carbohydrate-breath tests, which are non-specific, making it difficult to be sure that SIBO is the cause of the test result2,3,5. Upon giving a dose of either glucose or lactulose sugar, the level of hydrogen gas (produced by bacteria) is tested in the breath to determine bacterial numbers indirectly. However, if methane-producing bacteria are contributing to symptoms, a hydrogen-only breath test won’t accurately determine bacterial levels5. Due to this uncertainty around testing, it can be easy to dismiss SIBO as part of what’s driving digestive symptoms. In the scientific literature, the estimated prevalence of SIBO varies widely. Our lack of clear consensus around diagnosis is clouding our understanding of how big of a problem SIBO really is and may be hindering our progress in helping those with the condition.


    How SIBO occurs in the human body?

    There are multiple causes proposed to be at the root of SIBO. The first is associated with delayed or altered gastric motility2. Your gut is one long muscular tube that moves its contents through with a rhythmic, sweeping motion known as peristalsis. That sweeping motion, in addition to carrying nutrients, also helps to sweep bacteria along with it2. When something alters motility such as abdominal surgery or certain medications, it may give bacteria a stronger foothold in the small intestine. Also associated with altered motility are methane-producing bacteria. As they grow, their effects on the human gut may further their ability to multiply. Alternately, decreased stomach acid (due to age or the use of proton pump inhibitor medications for reflux) may also place you at risk because of your lowered antimicrobial defense in the upper digestive tract.


    How do I know if I have SIBO?

    Symptoms of SIBO are similar to that of irritable bowel syndrome (IBS) and include diarrhea, bloating and gas2. In more severe cases, malabsorption, anemia and weight loss may occur2. In fact, there is some controversy amongst researchers and practitioners as to how many diagnoses of IBS are really attributable to SIBO; in the literature, estimates vary between 4-78% of IBS sufferers2,3. Other digestive concerns such as celiac disease, Crohn’s disease and ulcerative colitis are also associated with SIBO1,.

    With SIBO bacterial overgrowth may lead to degradation of the gut barrier, which could in turn ramp up chronic inflammation3. This may help explain why conditions such as chronic fatigue syndrome and rosacea have links to SIBO2.

    When bloating occurs immediately during or after a meal, you may have to go back to your health care practitioner to talk about SIBO, as opposed to the delayed digestive reaction that is a hallmark of IBS.


    How is SIBO treated?

    While again, there is no gold-standard therapeutic approach to treating SIBO, there is an interesting treatment strategy available. Studies show that 1-2 courses of Rifaximin, a broad-spectrum, non-absorbable antibiotic may be effective at eradicating the overgrowth either on its own or in combination with another antibiotic2,3. Rifaximin is thought to decrease methane gas production; methane-producing bacteria may contribute to SIBO and the delayed gut motility that promotes it3.

    Of course, when using an antibiotic, a high-quality probiotic should be an essential part of your digestive support to help restore balance. Bio-K+ is Health Canada approved for use in concert with antibiotics; in addition, Bio-K+ contains three unique strains of Lactobacillus bacteria, a genus of bacteria that are found along the entire length of the digestive tract (including the small intestine) and are important for maintaining a healthy balance within the community. The unique liquid formula works the entire length of the gastrointestinal tract (not just the colon) allowing for the lactobacillus bacteria to gain exposure to the upper digestive tract, where they can assist in restoring health. Some physicians are wary of providing antibiotic therapy to their patients for digestive concerns due to worry about C.diff infection; again, Bio-K+ is an excellent ally in restoring microbiome balance as the only probiotic in Canada approved by Health Canada for primary prevention of C.diff infection due to antibiotic use.

    Few other treatment strategies for SIBO have been validated in the literature; in practice, reducing the availability of carbohydrate in the gut through a low FODMAP (Fermentable, Oligo-, Di-, and Mono-saccharides, and Polyols) protocol may be a wise treatment strategy. FODMAPs occur in grains like wheat, dairy products in the form of lactose and many of our healthiest foods such as garlic, apples and asparagus. FODMAPs are known to boost the growth of bacteria in the gut so eliminating them while on antibacterial therapy may help.

    Given that altered motility may promote bacterial overgrowth, theoretically, pro-kinetics may help although at this point their use has not been validated in SIBO. Pro-kinetics are foods or medication that are thought to help improve normal gut motility. Adding more naturally pro-kinetic foods like ginger or non-FODMAP fibres may be a worthwhile experiment.


    Living a pro-digestive lifestyle includes following a SIBO diet plan rich in high fibre plant foods, getting active, managing stress and taking a good quality probiotic daily. However, if you are having trouble getting to the bottom of your digestive symptoms, see your health care practitioner. In addition to examining common culprits like lactose intolerance, celiac disease and irritable bowel syndrome, talk to your doctor about testing for SIBO. It may just be the piece you were missing in your digestive puzzle.


    Do you have more questions about SIBO, gut health or probiotics? Let us know in comments below! For more information on digestive health, join our community. Click here to find your Bio-K+ closest point of sale. Contact us or find us on Facebook and Instagram.



    1. Differences in Microbiota Membership along the Gastrointestinal Tract of Piglets and Their Differential Alterations Following an Early-Life Antibiotic Intervention - PMC (
    3. Irritable bowel syndrome and small intestinal bacterial overgrowth: Meaningful association or unnecessary hype - PMC (

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    Desiree Nielsen Registered Dietitian
    About the author
    Desiree Nielsen is a registered dietitian, author and host of the vegetarian cooking sshow, The Urban Vegetarian. Desiree takes an evidence-based, integrative approach to her dietetics work, with a focus on anti-inflammatory, plant-centredcentered nutrition and digestive health.
    View all articles by Desiree Nielsen
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