Save 15% + FREE shipping when you Subscribe & Save. SHOP NOW

What is SIBO and Does SIBO Cause Digestive Issues in Kids?

Published January 24, 2024

share this article

Ever wondered why your kids are having frequent digestive troubles such as constipation? It might not be the "usual suspects," like lactose intolerance or simple indigestion. In some cases, your kids might be suffering from Small Intestinal Bacterial Overgrowth (SIBO). As an expert in pediatric gut health, I know navigating the symptoms from digestive issues in your little ones can be overwhelming. I’ve worked with many families that struggle with the same problems. Let’s break down what parents need to know about SIBO in kids — what it is, its causes, and treatment options.

What is SIBO?

SIBO (Small Intestinal Bacterial Overgrowth)  is a condition where an excessive number of normal intestinal bacteria from the large intestine move into the small intestine. In the appropriate location, bacteria play a crucial role in maintaining good health. For instance, in the large intestine, they contribute to the production of essential vitamins and short-chain fatty acids which helps support digestion. However, when it comes to the small intestine, an excessive bacterial population can increase the risk for digestive health challenges. 

Common Causes of SIBO in Kids

While the SIBO causes of kids vary from each kid, some common causes of SIBO include:

  • Poor Diet

Consuming a diet that lacks essential whole foods can significantly worsen SIBO symptoms. Additionally, the inclusion of refined sugars and unhealthy fats such as trans or saturated fats can further imbalance the gut's bacterial ecosystem, leading to an overgrowth of harmful bacteria in the small intestine. Trans and saturated fats can often be found in processed foods that contain partially hydrogenated oil such as fried foods, shortening, and certain baked goods [7]. Studies have also shown the effects of consuming canola oil can alter the structure of the microbiota, potentially contributing to [8].

  • Antibiotic Use

The frequent use of antibiotics can harm your little one’s gut flora. While antibiotics can remove bad bacteria, it can also remove the good ones as well.  Antibiotics can also cause yeast to overgrow because it kills the normal, good bacteria that prevents yeast overgrowth. Without enough good bacteria to support a healthy gut environment and keep candida yeast away, an overgrowth may occur and lead to symptoms of an infection.

  • Underlying Medical Conditions

Numerous factors could make a kid more susceptible to developing SIBO. Premature birth can result in an underdeveloped digestive system. This affects the establishment and development of the gut microbiota. An underdeveloped system cannot manage bacteria effectively [4]. 

Formula feeding, as opposed to breastfeeding, may introduce different bacterial strains that are harder for an infant’s microbiome to manage. Furthermore, if the mother was nutrient-deficient during pregnancy, the kid’s gut health could be impacted.

Symptoms of SIBO in Kids

Research has shown that kids with chronic gastrointestinal symptoms are more likely to have SIBO. In one clinical trial for the treatment of SIBO in kids, it was revealed that 91% of kids with chronic abdominal pain also had SIBO [1].  Kids with SIBO may also suffer from unintentional weight loss, food sensitivities, behavioral challenges, sleep, and a general failure to thrive [2,3].  Depending on the type of SIBO, a variety of these common symptoms may include:

    • Chronic Constipation. This is a frequent symptom to watch out for in kids with SIBO. The reason behind it is the excessive presence of specific bacteria that have a slowing effect on peristalsis—the natural, wave-like movements of the gut that help propel food and waste.

    • Abdominal Pain. Often dismissed as just another stomachache, abdominal pain in the case of SIBO is usually more consistent and pronounced. This discomfort arises from the increased gas production and pressure within the small intestine, which the surplus of bacteria generated. The pain can vary in intensity and is a clear sign that something is off in your little one’s digestive system.

    • Bloating. When it comes to SIBO, even small tummies can show noticeable distension or bloating. This is due to the accumulation of gasses like methane and hydrogen produced by the excess bacteria in the small intestine.

    • Diarrhea. While constipation is a common symptom, SIBO can also manifest as inconsistent bowel movements, swinging even to the extent of diarrhea. This occurs because the overgrowth of bacteria can interfere with the absorption of fats and carbohydrates, speeding up the transit of food and waste through the digestive system.

Treatment Options for SIBO

Treatment for SIBO will require combining several strategies including:

  • Dietary Changes.

    One of the most effective methods to combat SIBO are through dietary changes. Certain strains of E. coli, Klebsiella and Methanobrevibacter can overgrow when the diet is full of processed foods. Introducing a diet in your kiddos that is rich in fiber from fruits, vegetables, and whole grains can add beneficial prebiotic fiber to support gut health. The fiber from these foods support beneficial bacteria growth while helping to regulate bowel frequency. 

Simultaneously, reducing sugar intake is essential, as sugar feeds the bacteria above that contribute to SIBO. These dietary changes aim to balance the gut's microbiome, thus promoting a healthy environment for good gut bacteria to thrive.

Begin Health Expert Tip

For more details on Natural Remedies to Support SIBO in Kids, check out our blog here

  • Herbal Antibiotics

Unlike pharmaceutical antibiotics that negatively impact microbiome diversity by removing beneficial microbes, herbal antibiotics can target specific strains of bacteria without disrupting beneficial flora [6]. However, it's crucial to consult a healthcare provider for the appropriate dosage and regimen tailored to your kiddos needs

  • Prebiotic Fiber

A natural approach for constipation symptom relief is the inclusion of prebiotic fibers. Prebiotic fibers can naturally be found in plant foods such as carrots, leeks, and artichokes. However for pickier eaters, introducing a prebiotic supplement designed for toddlers and kids such as Growing Up Prebiotics can also help boost friendly bacteria count to rebuild a balanced microbiome. 


SIBO is a condition where an excessive number of normal intestinal bacteria from the large intestine move into the small intestine and causes digestive distress. Clinical data reveals a high occurrence of SIBO in kids with chronic abdominal issues. Common causes of SIBO include poor diet and antibiotic use. SIBO treatments often require multi-strategy approaches, often through diet changes. Incorporating prebiotics supplements such as Begin Health’s Growing Up Prebiotics can be helpful to help boost the friendly gut-bacteria to restore digestive balance.


[1] M1215 Double-Blind Placebo Controlled Trial of Xifaxan for the Treatment of Small Intestinal Bacterial Overgrowth in Children With Chronic Abdominal Pain
Collins, Brynie S. et al. Gastroenterology, Volume 138, Issue 5, S-356

[2] McGrath, K., Pitt, J., & Bines, J. E. (2019b). Small intestinal bacterial overgrowth in children with intestinal failure on home parenteral nutrition. JGH Open, 3(5), 394–399.

[3] Fabregat, M. I. P., Gardner, R., Hassan, M. A., Kapphahn, K., & Yeh, A. M. (2022). Small intestinal bacterial overgrowth in children: Clinical features and treatment response. JPGN Reports, 3(2), e185.

[4] Arboleya, S., Rios-Covian, D., Maillard, F., Langella, P., Gueimonde, M., & Martín, R. (2022). Preterm delivery: microbial dysbiosis, gut inflammation and hyperpermeability. Frontiers in Microbiology, 12.

[5] Chedid, V., Dhalla, S., Clarke, J. O., Roland, B. C., Dunbar, K. B., Koh, J., Justino, E., Tomakin, E., & Mullin, G. E. (2014). Herbal Therapy is Equivalent to Rifaximin for the Treatment of Small Intestinal Bacterial Overgrowth. Global Advances in Health and Medicine, 3(3), 16–24.

[6] Patangia DV, Anthony Ryan C, Dempsey E, Paul Ross R, Stanton C. Impact of antibiotics on the human microbiome and consequences for host health. Microbiologyopen. 2022 Feb;11(1):e1260. doi: 10.1002/mbo3.1260. PMID: 35212478; PMCID: PMC8756738.

[7] Ruan, M., Bu, Y., Wu, F., Zhang, S., Chen, R., Li, N., Liu, Z., & Wang, H. (2021). Chronic consumption of thermally processed palm oil or canola oil modified gut microflora of rats. Food Science and Human Wellness, 10(1), 94–102.