SIBO (Small Intestine Bacterial Overgrowth)

What Are SIBO and SIFO?

SIBO stands for Small Intestine Bacterial Overgrowth, a gastrointestinal condition characterized by an excessive rise in the population of bacteria in the small intestine—bacteria that are typically found in greater numbers in the large intestine (colon). SIFO (Small Intestine Fungal Overgrowth) is a similar condition characterized by excessive fungi in the small intestine. With SIBO and SIFO, these microorganisms multiply in the upper part of the gut where the environment is normally less populated. Symptoms of SIBO and SIFO can include:

• Nutrient deficiencies (due to bacterial interference with absorption)
• Unexplained weight loss
• Failure to thrive
• Fatigue and general malaise

Over time, SIBO and SIFO can damage the intestinal lining, leading to leaky gut, inflammation, and systemic symptoms. This bacterial overactivity can ferment undigested carbohydrates, leading to excess production of gas, causing the symptoms listed above. Methane-producing bacteria are often associated with constipation, whereas hydrogen-producers more commonly cause diarrhea.

What Condition(s) Lead to SIBO and SIFO?

SIBO and SIFO are not simply a matter of “bad microorganisms” multiplying, but rather a sign that the regulatory systems of the digestive tract have been disrupted. The primary factors include:

Low Ileocecal Valve Pressure

Research (see Sources & References, below) has shown a significant association between SIBO and low ileocecal valve pressure. This valve plays a critical role in maintaining proper gastrointestinal function by regulating the one-way flow of contents from the small intestine to the large intestine. Dysfunction of this valve, particularly when it remains open for prolonged periods or fails to close properly, can lead to the backflow of colonic contents, including bacteria, into the small intestine.

Low Stomach Acid

Low stomach acid, also known as hypochlorhydria, is a recognized contributing factor to the development of SIBO (see Sources & References, below). Stomach acid serves as a primary defense mechanism by killing harmful bacteria and preventing their migration from the stomach into the small intestine, where they do not belong. When stomach acid levels are insufficient, bacteria can survive the less-acidic environment of the stomach and colonize the small intestine, leading to SIBO and/or SIFO. Children who take proton-pump inhibitors are more likely to develop SIBO.

Impaired Motility of the Small Intestine

Motility refers to the wave-like muscle contractions (peristalsis) that move food along the digestive tract. In healthy children, this helps flush bacteria towards the colon, preventing overgrowth in the small intestine. Anything that slows these contractions can allow bacteria to remain, set up shop, and multiply in the wrong place. Conditions or states that slow motility can include:

• Hypothyroidism
• Mitiochondrial dysfunction
• Previous intestinal surgery or anatomical changes
• Certain medications (e.g. opiates, some anticholinergics)

The Fight-or-Flight Response

Chronic activation of the sympathetic nervous system—the body’s fight-or-flight stress mode—causes digestion to slow. In a true emergency, the body directs energy and blood away from the gut to muscles and the brain. When this stress state becomes chronic (as is the case with many modern lifestyles), it essentially keeps the gut in “pause” mode. Over time, this can result in:

• Delayed stomach emptying (gastroparesis)
• Slowed transit time through the small intestine
• Greater opportunity for bacteria to multiply where they shouldn’t

Impaired Vagal Tone

The vagus nerve is a major component of the parasympathetic nervous system, coordinating rest, digestion, and repair. Healthy vagal tone means this nerve is active and able to stimulate the rhythmic contractions of the intestines. If vagal tone is poor—due to chronic stress, trauma, illness, chronic infections, or even aging—the digestive tract becomes sluggish. This is often seen in people with long-standing diabetes (due to neuropathy), but also in those with chronic Lyme disease, mold illness, and autoimmune conditions.

Processed, Low-Fiber Diet

Modern, processed diets—high in refined sugars, starches, and lacking in fiber—fuel overgrowth of bacteria by providing a constant source of fermentable carbohydrates. Such diets not only feed the wrong bacteria, but also do little to encourage normal motility because they tend to lack volume and the indigestible fiber that stimulates movement.

Antibiotic Use and Gut-Flora Imbalance

While antibiotics may sometimes be deemed as necessary, their overuse is strongly associated with disruption of normal gut flora, allowing opportunistic bacteria to take over, sometimes in inappropriate locations such as the small intestine.

What Are Ways of Addressing SIBO and SIFO?

Addressing SIBO and SIFO requires a multi-pronged approach that restores both the ecology and function of the digestive tract, not just killing excess bacteria. The following suggestions may improve symptoms of SIBO/SIFO for your child.

Improving Motility

Because slowed motility is a root cause, restoring normal muscle contractions should be a priority. Strategies include:

• Dietary modification: Remove trigger foods that can irritate the gut or slow motility, and focus on easily digestible, whole foods.
• Staying physically active: Moderate, regular exercise naturally stimulates gut movement.
• Magnesium supplementation: Magnesium citrate or oxide can help some children move their bowels more regularly, counteracting constipation and stagnation. Epsom salt baths can help those who struggle with taking supplements orally.
• Prokinetic herbs and supplements: Certain substances, such as ginger, may naturally encourage peristalsis.
• Improving vagal tone: Motility also relies on cilia (smaller hair-like projections) in various parts of the body to move bacteria along – gargling, humming or making a buzzing sound can all improve vagal tone and improves access to the rest and digest (parasympathetic) state. More strategies for this are listed below.

Lowering the Fight-or-Flight Response by Improving Vagal Tone

Chronic stress must be addressed to enable healing. When the body is stuck in fight-or-flight mode, digestion simply can’t work optimally. Ways to reduce sympathetic nervous system dominance and increase vagal tone include:

• Mindfulness practices: Meditation, deep diaphragmatic breathing, yoga, qi gong and tai chi can lower stress.
• Adequate and restful sleep: Children need more sleep than adults. Aim to align your child’s circadian rhythm with the natural rhythm of the sun. Getting early morning sunlight can help reset your child’s rhythm.
• Reducing stimulants: Have your child avoid blue lights and screen exposure after the sun goes down, as these can disrupt circadian rhythm.
• Gargling or singing loudly: These actions stimulate the muscles innervated by the vagus nerve.
• Acupuncture: This healing modality can calm a child’s nervous system, thus potentially improving vagal tone and peristalsis.
• Devices: Newer gadgets such as the Apollo Neuro are designed to promote calm in a safe and gentle way.
• Chiropractic care: Chiropractic adjustments address underlying spinal misalignments that can disrupt nerve function that affect digestive system activity. Spinal misalignments, or subluxations, can interfere with nerve signals to the digestive organs, potentially contributing to digestive dysfunction.
• Eating in a peaceful environment: The gut is not only less efficient at moving bugs around but “leakier” and prone to dysbiosis when children eat under stress such as family arguments at the table or rushed eating or incomplete chewing.

Improving the Timing of Stomach Acid

If your child has been prescribed proton-pump inhibitors for acid reflux or GERD, you may want to work with a more holistic practitioner who understands how to improve reflux symptoms with the elimination of problematic foods such as dairy and with the addition of stomach-acid promoting foods such as apple cider vinegar before a meal.

Herbal Medicine

Some herbs are antimicrobial active and/or gut-soothing herbs. They can:

• Suppress the overgrowth of unwanted bacteria
• Promote growth of beneficial flora
• Heal the intestinal lining and reduce inflammation

Some top herbs and herbal strategies include:

• Berberine: Derived from goldenseal and other plants, it’s well-studied for its antimicrobial effects in the gut, and may reduce SIBO populations without broadly disrupting good flora.
• Dandelion root: Supports bile flow and has mild antimicrobial action, which can be especially beneficial for improving fat digestion and gently encouraging gut cleansing.
• Slippery elm: Supplies mucilage, a gel-like fiber that soothes and restores the intestinal mucous lining, aiding both healing and protection.
• Garlic: Used in capsule form to bypass the stomach, garlic’s active compounds can help curb bacterial overgrowth all the way to the colon (though it may irritate some sensitive stomachs).
• Adaptogens: Ashwagandha and other adaptogenic herbs help the body respond to stress, lowering fight-or-flight and promoting parasympathetic (rest-repair-digest) dominance.

Listen in here at 01:35:47 to hear Bill Rawls MD discuss how these herbs and other interventions can help with SIBO.

Importantly, herbal regimens need to be tailored to each individual, as some children—with extreme gut sensitivity—may need to start at much lower doses and progress very slowly. Find a practitioner in our directory here.

Using Non-Fermentable Fiber

Fiber is essential for motility and healthy elimination, but not all fibers are created equal—some ferment quickly, producing gas and worsening SIBO symptoms. Non-fermentable fiber adds bulk and promote movement without excessive fermentation. Examples of this type of fiber are:

• Acacia: Gentle on the gut and rarely causes gas, acacia gum feeds beneficial bacteria and moves things along.
• Partially hydrolyzed guar gum (PHGG): This low-FODMAP fiber found in supplements such as Sunfiber that generally well-tolerated for those with SIBO.
• Flaxseed meal: Adds volume and lubrication to stool. It is best bought whole and stored in the refrigerator to prevent rancidity. Grind it yourself and add a small amount to your child’s food.

This type of fiber should be started gradually and increased as tolerated, ensuring adequate hydration.

Using the Low-FODMAPS Diet

FODMAPS are Fermentable Oligosaccharides, Disaccharides, Monosaccharides And Polyols—a group of short-chain carbohydrates that are easily fermented by gut bacteria. Many people with SIBO find that restricting high-FODMAP foods reduces their symptoms dramatically. Common high-FODMAP foods include:

• Dairy containing lactose
• Sweeteners such as xylitol, sorbitol, and mannitol

By reducing these foods, you can starve the overgrown bacteria and lessen gas and bloating. The goal is not to remain on a low-FODMAP diet forever, but to use it as a short-term reset while working to restore broader gut function—improving motility, repairing the lining, and ultimately rebuilding a healthy, diverse population of gut bacteria. Learn more about the diet here.

A Restorative Approach to SIBO and SIFO

Patience is necessary for alleviating SIBO symptoms, as healing can take months and often proceeds in stages. For some, using the help of qualified integrative or functional medicine practitioners who blend conventional and natural therapies can be invaluable. Most importantly, restoring gut health means restoring whole-body health—when the digestive system is functioning and balanced, energy, mood, and resilience can improve across the board.

SIBO is not just a random bacterial problem, but a reflection of broader system imbalances—in motility, stress, nervous system regulation, and diet. By addressing these root causes with a combination of calming the nervous system, supporting healthy gut movement, using targeted herbal therapy, the right fibers, and dietary adjustments, long-term digestive health and systemic well-being becomes an achievable goal.

About Maria Rickert Hong CHHC

Prior to working on Wall Street, she was a marketing specialist for Halliburton in New Orleans, where she also received her MBA in Finance & Strategy from Tulane University.

She is the author of the bestselling book Almost Autism: Recovering Children from Sensory Processing Disorder and the co-author of Brain Under Attack: A Resource for Parents and Caregivers of Children with PANS, PANDAS, and Autoimmune Encephalitis. She is a co-author of Reversal of Autism Symptoms among Dizygotic Twins through a Personalized Lifestyle and Environmental Modification Approach: A Case Report and Review of the Literature, J. Pers. Med. 2024, 14(6), 641.

Maria is also a Certified Holistic Health Counselor. Her work can be found on DocumentingHope.com, Healing.DocumentingHope.com, Conference.DocumentingHope.com and MariaRickertHong.com

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