Prebiotics and Probiotics for Kids with SIBO

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Small intestinal bacterial overgrowth (SIBO) is on the rise in children, and if left untreated, may cause serious health problems. While the conventional view of SIBO has been that prebiotics and probiotics should be avoided, recent studies suggest that not only are prebiotics and probiotics not harmful for people with SIBO, but they may actually be helpful. Read on to learn about why you should consider incorporating prebiotics and probiotics into treatment protocols for your pediatric SIBO patients.

The Conventional View of SIBO

Small intestinal bacterial overgrowth (SIBO) is a functional gastrointestinal disorder in which excessive bacteria are present in the small intestine. (1) For many years, the conventional view in the SIBO world has been that prebiotics and probiotics should be avoided, including fermented foods and fermentable fibers; this is based on the rationale that since SIBO involves an overgrowth of bacteria in the small intestine, consuming live bacteria (probiotics) or substances that feed bacteria already in the gut (prebiotics) would be harmful.

However, this hesitation has been based on the empirical experience of clinicians testing for and treating SIBO. Recently, studies have emerged suggesting that not only are probiotics and prebiotics not harmful in people with SIBO, they may even be helpful. (2)

Prebiotics and Probiotics May Be Helpful for SIBO

Contrary to conventional recommendations, a growing body of evidence indicates that a combination of prebiotics and probiotics may be beneficial for people with SIBO.

Research demonstrates that prebiotics and probiotics crowd out pathogenic bacteria in the gut, produce natural antibacterial substances, inhibit bacterial translocation, strengthen the immune system, reduce inflammation, and increase gut motility.

These mechanisms help explain the new evidence suggesting that prebiotics and probiotics reduce symptoms of SIBO. (3) A study of probiotic treatment specific for SIBO found that administration of the probiotic Bacillus clausii was comparable to antibiotics for normalizing hydrogen breath tests. (4) In another small study, Lactobacillus casei and Lactobacillus acidophilus were found to be effective for treating diarrhea caused by bacterial overgrowth. (5) A small pilot study found that a probiotic containing Lactobacillus casei, Lactobacillus plantarum, Streptococcus faecalis, and Bifidobacterium brevis was more effective at reducing abdominal distension in SIBO patients compared to the antibiotic metronidazole. (6)

Another pilot study found that a 15-day course of the prebiotic FOS and Bacillus coagulans produced significant improvements in SIBO symptoms after an initial three-week course of broad-spectrum antibiotics. (7) In another study that combined antibiotics with prebiotics and probiotics, it was discovered that administration of rifaximin for seven days, followed by either seven days of Lactobacillus casei or FOS, led to a significant improvement in SIBO symptoms. (8)

Therefore, while the evidence is not conclusive, it appears that prebiotic and probiotic treatment for SIBO may be most effective when used after an initial course of antibiotics. While studies on prebiotic and probiotic treatment for SIBO are limited, the available evidence is encouraging and provides substantial grounds for further research.

SIBO in Children

The prevalence of SIBO in children is higher than previously believed. (9) SIBO may have especially harmful consequences for children due to the malabsorptive state it causes in the small intestine, which can lead to deficiencies in vitamins, minerals, and macronutrients that are crucial for physical growth and development.

Prebiotics and probiotics are helpful, not harmful, for treating SIBO. #probiotics #guthealth

Prebiotics and probiotics may be especially useful treatment options for children with SIBO, as they do not carry the risk of causing diarrhea, C. difficile, allergic reactions, and antibiotic resistance. Before examining the emerging research on prebiotic and probiotic treatment for SIBO in kids, let’s cover some basic information about the potential causes of SIBO in children and the health consequences of untreated SIBO.

What Causes SIBO in Children?

A variety of factors may cause children to develop SIBO. Certain pre-existing health conditions, early childhood risk factors, and the use of certain pharmaceutical drugs may predispose children to SIBO. The common denominator among these factors is that they disrupt mechanisms that normally inhibit bacterial overgrowth in the small intestine.

Pre-Existing Health Conditions

Several pre-existing health conditions may predispose children to SIBO. (10) Abnormalities in the structure of the GI tract, motility disorders, depressed thyroid function, and mitochondrial disorders decrease small intestine motility, causing food and ingested bacteria to stagnate, which may promote bacterial overgrowth. (11, 12) Lowered immunity may also predispose children to SIBO by disrupting normal immune mechanisms in the intestine that keep bacterial counts in check. (13)

Early Childhood Risk Factors

Development of the intestinal microbiome begins in infancy and involves an exchange of microbes between mother and child. Practices that affect this exchange, such as the use of antibiotics during pregnancy, birth by C-section, perinatal antibiotics, and formula feeding, alter the infant microbiome and may predispose a child to dysbiosis and SIBO down the road. (14, 15, 16, 17)

Pharmaceutical Drug Use

Pharmaceutical drugs, including antibiotics, proton pump inhibitors, and H2 receptor blockers, are linked to the development of SIBO in children. Antibiotic use wipes out beneficial gut microbes, increasing the risk of intestinal dysbiosis. (18) Proton pump inhibitors (PPIs) and H2 receptor blockers increase the risk of SIBO by decreasing gastric acid secretion, which is needed to suppress the growth of ingested bacteria. Infants and children are increasingly being prescribed PPIs for GERD, reflux, and colic, and there is a strong association between the use of these drugs and the development of SIBO in children. (19, 20, 21) Concerningly, research indicates that children are at risk of SIBO even after very short-term PPI treatment. (22, 23, 24, 25)

Long-Term Consequences of SIBO in Children

SIBO may have serious health consequences in children. SIBO impairs the intestinal absorption of fats, proteins, carbohydrates, and fat-soluble vitamins, thus depriving a child of these nutrients at a time during which optimal nutrition is crucial for promoting growth and development. (26) SIBO also increases intestinal permeability, a condition that has been linked to systemic inflammation, malnutrition, and growth stunting in children. (27) In addition, untreated SIBO may cause weight loss, retarded growth, iron deficiency anemia, vitamin D deficiency, vitamin B12 deficiency, hypocalcemia, and in severe cases, osteoporosis. (28) It is crucial that children with SIBO be treated promptly to prevent these serious complications.

Prebiotic and Probiotic Treatment May Be Ideal for Kids with SIBO

In adults, the mainstay treatment for SIBO is antibiotic therapy. However, research supporting the use of antibiotics for pediatric patients with SIBO is severely lacking. (29) There are legitimate concerns about the use of antibiotics in children, especially on a recurring basis, as may be required with SIBO treatment. Antibiotics have many side effects, including diarrhea, Clostridium difficile infection, toxic and allergic reactions, and disruption of the gut microbiota.

Considering the lack of evidence supporting antibiotic treatment for children with SIBO, novel treatment options are needed.

Fortunately, emerging research suggests that probiotics and prebiotics may be an ideal alternative to antibiotics for children with SIBO, producing improvements in symptoms without adverse side effects. 

While evidence supporting the potential of prebiotics and probiotics in adults has been accumulating for several years, up until recently, there were no studies examining the efficacy of prebiotics and probiotics for SIBO specifically in children.

However, a recent study found that administration of a synbiotic (a product containing both a prebiotic and a probiotic) produced significant improvement of SIBO symptoms in children, including postprandial abdominal swelling, distension, mucus in stool, constipation, and diarrhea, without any adverse effects. (30) The synbiotic contained Bifidobacterium lactis and inulin.

This study, combined with the studies on adults with SIBO mentioned previously, further supports the idea that prebiotics and probiotics should be embraced, rather than avoided, in the treatment of SIBO.

Conflicting Evidence Regarding FODMAPs and SIBO

This new research supporting prebiotic and probiotic therapy for SIBO raises some important questions. There is good evidence indicating that a low-FODMAP diet is useful for reducing SIBO symptoms such as bloating, diarrhea, and constipation; (31, 32) however, this directly contradicts the evidence laid out here supporting the use of prebiotics (a type of fermentable fiber) for SIBO treatment.

In another apparent contradiction, SIBO patients are often told to avoid fermented foods, yet the research indicates that probiotics help decrease SIBO symptoms. Could these contradictions have to do with individual differences in tolerance of FODMAPs and fermented foods? Could it be that people who have already undergone antimicrobial treatment respond better to prebiotics and probiotics? Could prebiotics and probiotics still be helpful for kids who have not undergone antimicrobial treatment?

Until more conclusive evidence is available to help us answer these questions, dietary experimentation may be necessary in order to determine an individual’s tolerance for fermented foods and FODMAPs while undergoing SIBO treatment.

Vagus Nerve Stimulation May Prevent SIBO Recurrence

A final therapy that is worth mentioning and may nicely complement prebiotic and probiotic therapy for SIBO is vagus nerve stimulation (VNS). Research indicates that low vagal nerve tone alters the migrating motor complex in the gut, reducing gastrointestinal motility and thus allowing bacteria to flourish in the small intestine. VNS has been found to increase gastrointestinal motility and gastric acid production, both of which are important factors for preventing SIBO. (33, 34)

While VNS was originally only available via invasive devices implanted under the skin, there are a couple of non-invasive vagus nerve-stimulating devices available to consumers. These include Nervana (no affiliation), a device that combines vagus nerve stimulation with relaxing music, and pulsed electromagnetic field (PEMF) therapy, which is offered in the form of a handheld device through MicroPulse (no affiliation).

However, these devices are expensive, and may not be the best choice for everyone. For those looking for a more cost-conscious option, acupuncture and massage may be  good choices, since both of these modalities stimulate the vagus nerve.

Finally, the practice of certain exercises, such as gargling and stimulating the soft palate with a tongue depressor, have been found to stimulate the vagus nerve. Patients may want to consider working under the supervision of a healthcare practitioner trained in vagus nerve stimulation, such as a functional neurologist, who can provide vagus nerve stimulation using devices that are not available direct to consumer.

Whichever route a patient chooses to take, restoration of GI motility and gastric acid production through VNS  may nicely complement prebiotic and probiotic SIBO treatment in children.


  1. I have been told that prebiotics enhance the good bacteria in the gut BUT ALSO enchance the bad bacteria so it is a no win situation. Is there any truth to this?? In reality it makes sense bevause how would the FOS/Inulin or whatever distinguish between the two and if you already have an overgrowth of bad bacteria wouldn’t it make SiBO worse instead of better., rather than getting a good probiotic with the correct strains (???) without the added prebiotic.

    Please advise as i am stumped as what to do. Thank you.

  2. I have been told that prebiotics enhance the good bacteria in the gut BUT ALSO enchance the bad bacteria so it is a no win situation. Is there any truth to this?? In reality it makes sense bevause how would the FOS/Inulin or whatever distinguish between the two and if you already have an overgrowth of bad bacteria wouldn’t it make SiBO worse instead of better., rather than getting a good probiotic with the correct strains (???) without the added prebiotic. Also what probiotic strains are good for SIBO and could you recommend a brand to take minus the prebiotic.

    Please advise as i am stumped as what to do. Thank you.

  3. Thanks Chris. Great article. I’m wondering if you have used antimicrobial herbs for treating kids with SIBO. I’m a functional medicine practitioner and am working with a 4 year old. His Methanobrevibacter smithii stool count was elevated and he has an autoimmune disease. I’m considering a low dose Candibactin AR and BR but was wondering if you think that is safe for children.

  4. Hi

    I have sibo, mfthr , lowish thyroid… have pa in family…

    My son is 3.5 years when born ended up dairy free milk and gluten free.. was better …

    Then had delays so put back to normal diet to see if helped …

    He is now getting constipated, mood swings, irritable, looks pale, lashing out still has speech delay…

    Has wriggly nights sleep is tiered a lot and seems to want sugar when didnt before and lifts his mood back up to normal … didn’t have sugar before I n gluten free..

    He is worse with bread , I think also yeast..

    He seems to have some asd traits more so after bread..

    It’s not celiac and sibo not mentioned but he seems just like me with symptoms …

    I think Yes affecting his development what ever is going on …

    What can I do I know sibo is more than just gluten but he has s fussy any way so can’t do very strict diet but at same time he ate regular with gluten and dairy free but I think the vitamins in baby milk was helping when little …

    As he perks up with vitamins 🙁