Pediatric Gut Health & Digestive Issues: A Functional Medicine Protocol

The Garden You Plant in the First Thousand Days

A child’s gut is not a smaller version of an adult gut. It is a garden being planted for the first time — every seed matters, every disruption echoes forward. The microbiome a child develops in the first three years of life becomes the template for immune function, neurodevelopment, mood regulation, and metabolic health for decades to come.

Conventional pediatrics often treats digestive symptoms in children with symptom suppression — acid blockers for reflux, Miralax for constipation, antibiotics for everything. Functional medicine asks the deeper question: why is this child’s gut not functioning properly, and what does it need to heal?

The Institute for Functional Medicine (IFM) positions the gut as the foundational node in its matrix model. In pediatrics, this is amplified — a compromised gut in a developing child doesn’t just cause digestive symptoms. It shapes the trajectory of that child’s entire biology.

Colic: The First Signal of Dysbiosis

Colic — defined as inconsolable crying for more than three hours a day, more than three days a week — affects up to 25% of infants. For generations, it was dismissed as a mystery that babies “grow out of.” Functional medicine sees colic differently: it is often the first clinical expression of gut dysbiosis.

Dr. Francesco Savino’s landmark research at the University of Turin changed the conversation. His 2007 study published in Pediatrics demonstrated that the probiotic strain Lactobacillus reuteri DSM 17938 significantly reduced crying time in breastfed colicky infants compared to simethicone. His follow-up 2010 study confirmed these findings — infants receiving L. reuteri showed a 50% reduction in crying time within one week, with 95% of treated infants achieving this threshold by day 21.

The mechanism is elegant. Colicky infants consistently show lower counts of Lactobacilli and higher counts of gas-producing coliforms and Proteobacteria. L. reuteri DSM 17938 reduces gas production, modulates gut motility, and decreases visceral pain signaling through the vagus nerve.

Protocol for infant colic:

• L. reuteri DSM 17938: 5 drops daily (10^8 CFU), given directly or mixed into expressed breast milk
• Maternal elimination of cow’s milk protein (if breastfeeding) — trial for 2-4 weeks
• Assess for tongue tie and latch issues contributing to aerophagia
• Gentle abdominal massage and bicycle legs for gas relief

Infant Reflux: Root Causes vs. PPI Overuse

Infant reflux has become one of the most over-medicated conditions in pediatrics. Proton pump inhibitors (PPIs) like omeprazole are now prescribed to infants as young as two months, despite multiple studies — including the landmark Orenstein 2009 study in Journal of Pediatrics — showing PPIs are no more effective than placebo for infant reflux symptoms.

Worse, PPIs in infants are associated with increased risk of respiratory and gastrointestinal infections, altered gut microbiome composition, reduced nutrient absorption (calcium, magnesium, iron, B12), and increased risk of food allergies.

Most infant reflux is physiological — an immature lower esophageal sphincter that resolves by 12-18 months. When reflux is truly pathological, the functional approach investigates:

• Cow’s milk protein allergy or sensitivity — the most common dietary trigger, present in up to 40% of infants with significant reflux
• Overfeeding — smaller, more frequent feeds reduce gastric distension
• Gut dysbiosis — abnormal fermentation patterns increase intra-abdominal pressure
• Food sensitivities transmitted through breast milk — dairy, soy, wheat, eggs
• Formula composition — intact casein proteins vs. hydrolyzed or amino acid formulas

Before reaching for acid blockers, try:

• Maternal elimination diet (dairy first, then soy) for 2-4 weeks if breastfeeding
• Upright positioning for 20-30 minutes after feeds
• L. reuteri DSM 17938 (5 drops daily)
• Consider partially hydrolyzed or extensively hydrolyzed formula if formula-fed
• Reassess at 4, 8, and 12 months — most physiological reflux resolves spontaneously

Pediatric SIBO and Motility Disorders

Small intestinal bacterial overgrowth (SIBO) in children is underdiagnosed and often misclassified as “functional abdominal pain” or irritable bowel syndrome. Dr. Mark Pimentel’s work at Cedars-Sinai has shown that impaired migrating motor complex (MMC) function — the “housekeeper wave” that sweeps bacteria from the small intestine during fasting — is a primary driver of SIBO.

In children, MMC disruption can follow:

• Gastroenteritis (post-infectious SIBO) — the most common trigger
• Antibiotic overuse disrupting the commensal ecosystem
• Ileocecal valve dysfunction
• Opioid use (post-surgical)
• Hypothyroidism

Pediatric SIBO symptoms often present as:

• Bloating and distension after meals
• Alternating diarrhea and constipation
• Abdominal pain — often periumbilical
• Failure to thrive in severe cases
• Behavioral irritability (gut-brain axis activation)

Testing: Lactulose breath test — adapted for children with age-appropriate lactulose dosing (typically 10g for children under 30kg vs. 20g for older children/adults).

Treatment approach:

• Herbal antimicrobials adapted for pediatric dosing: oregano oil (enteric-coated, age 6+: 50-100mg twice daily with meals), berberine (age 8+: 100-200mg twice daily), or allicin (age 4+: 100-200mg twice daily)
• Rifaximin remains an option for children over 12 (200mg three times daily for 14 days)
• Prokinetics to restore MMC: ginger (50-100mg standardized extract with dinner), or low-dose erythromycin (2-3mg/kg at bedtime, prescription)
• Spacing meals 4-5 hours apart to allow MMC cycling — this means reducing grazing and snacking

Constipation Beyond Miralax

Polyethylene glycol (Miralax/PEG 3350) has become the reflexive prescription for pediatric constipation. While it draws water into the stool, it does nothing to address why the child is constipated. The FDA has never approved Miralax for use in children, and a 2008 citizen petition raised concerns about potential neuropsychiatric side effects — a concern that prompted an ongoing FDA-funded study at Children’s Hospital of Philadelphia.

Functional root causes of pediatric constipation include:

• Magnesium deficiency — widespread in children eating processed food diets
• Insufficient fiber and water intake — obvious but persistently undertreated
• Dairy sensitivity — cow’s milk protein is the single most common cause of chronic constipation in children (Iacono 1998, NEJM)
• Hypothyroidism — even subclinical
• Gut dysbiosis — low Bifidobacteria, low butyrate production
• Pelvic floor dyssynergia — particularly in children with withholding behavior
• Iron supplementation — ferrous sulfate is notoriously constipating

Functional constipation protocol:

• Magnesium citrate or glycinate: 2-4mg/kg/day, titrate to soft daily stool (typically 50-100mg for toddlers, 100-200mg for school-age)
• Vitamin C: 250-500mg daily — osmotic effect plus antioxidant support
• Adequate water: half the child’s body weight (in pounds) in ounces of water daily
• Fiber: ground flax (1-2 tsp daily in smoothies), chia seeds, cooked vegetables
• Probiotics: Bifidobacterium lactis BB-12 or Lactobacillus rhamnosus GG — 5-10 billion CFU daily
• Dairy elimination trial: strict removal of all cow’s milk protein for 4 weeks
• Squatty stool or foot support for toilet positioning
• If on iron: switch from ferrous sulfate to iron bisglycinate (Ferrochel) — far less constipating

Food Sensitivities in Children

The food sensitivity landscape in children is fraught with controversy, particularly around IgG testing. The American Academy of Allergy, Asthma & Immunology (AAAAI) formally advises against IgG food sensitivity panels, arguing that IgG represents normal immune exposure, not pathology.

Yet clinically, functional medicine practitioners see children whose eczema clears, whose behavior stabilizes, and whose chronic congestion resolves when IgG-reactive foods are removed. The truth likely sits in the middle: IgG testing is not a definitive diagnostic tool, but in the context of intestinal permeability (leaky gut), elevated IgG to specific foods can serve as a useful clinical signal — a map of what’s crossing an impaired barrier.

The gold standard remains the elimination diet. For children, this must be adapted:

• Standard elimination (age 2+): Remove gluten, dairy, eggs, soy, corn, and refined sugar for 3-4 weeks, then reintroduce one food every 3-4 days while tracking symptoms
• Simplified elimination (toddlers): Remove dairy and gluten only for 3-4 weeks — these two cover the majority of pediatric food reactions
• Track symptoms across domains: digestive (bloating, stool changes), skin (eczema flares, rashes), behavioral (irritability, hyperactivity, poor sleep), respiratory (congestion, ear infections)

Critical practical points for parents:

• The elimination phase must be complete — hidden dairy in bread, soy in packaged foods, gluten in sauces all invalidate the trial
• Behavioral and mood changes often take the full 3-4 weeks to manifest
• Reintroduction reactions may be delayed 24-72 hours
• A food that causes a reaction can often be reintroduced successfully after 3-6 months of gut healing

Leaky Gut in Children

Intestinal permeability — “leaky gut” — is not a fringe concept. Dr. Alessio Fasano at Massachusetts General Hospital has published extensively on zonulin, the protein that modulates tight junctions between intestinal epithelial cells. His work demonstrates that increased intestinal permeability precedes and contributes to autoimmune conditions, allergies, and neurological symptoms.

In children, leaky gut commonly manifests as:

• Eczema and atopic dermatitis — the skin reflecting gut barrier dysfunction
• Behavioral changes — irritability, brain fog, anxiety, aggression
• Food reactions — increasing number of reactive foods over time
• Recurrent infections — immune dysregulation from chronic gut inflammation
• Failure to thrive — nutrient malabsorption

Triggers of intestinal permeability in children:

• Antibiotic use (even a single course disrupts the microbiome for months)
• NSAIDs (ibuprofen — routinely given for fevers)
• Gluten (via zonulin release, even in non-celiac individuals — Fasano 2011)
• Gut infections (parasites, pathogenic bacteria, Candida overgrowth)
• Chronic stress (cortisol degrades mucosal integrity)
• Cesarean birth and formula feeding (altered microbiome colonization)

Gut healing protocol for children (adapted 5R framework):

1. Remove: Identified food triggers, infections, toxins
2. Replace: Digestive enzymes if needed (plant-based, half adult dose)
3. Reinoculate: Age-appropriate probiotics (see below) plus prebiotic fiber
4. Repair: L-glutamine (50-100mg/kg/day, max 2-5g depending on age), zinc carnosine (age 6+: 25-50mg daily), colostrum (1-2g daily), bone broth or gelatin
5. Rebalance: Sleep, stress reduction, movement, outdoor time

Probiotics by Age: A Developmental Approach

Not all probiotics are created equal, and children at different developmental stages need different microbial support.

Newborn to 6 months:

• Lactobacillus reuteri DSM 17938 — 5 drops daily (10^8 CFU)
• Bifidobacterium infantis EVC001 — supports HMO metabolism in breastfed infants
• Delivery: drops directly in mouth or on nipple before feeding

6 months to 2 years:

• Lactobacillus rhamnosus GG — 5 billion CFU daily
• Bifidobacterium lactis BB-12 — 5 billion CFU daily
• Begin introducing prebiotic-rich foods: cooked and cooled sweet potato, banana, oats

2 to 5 years:

• Multi-strain formulations — 5-10 billion CFU daily
• Include Lactobacillus and Bifidobacterium species
• Saccharomyces boulardii — 250mg daily during and after antibiotic courses
• Prebiotic fiber: ground flax, cooked and cooled rice, Jerusalem artichoke, garlic, onion

6 to 12 years:

• Multi-strain — 10-20 billion CFU daily
• Can begin soil-based organisms (Bacillus coagulans, Bacillus subtilis) — 1-2 billion CFU daily
• Prebiotic fiber goal: 15-20g daily from whole food sources
• S. boulardii — 250-500mg daily during antibiotic exposure

Adolescents (13+):

• Adult formulations appropriate — 20-50 billion CFU daily
• Full range of prebiotic fibers including resistant starch, inulin, FOS, GOS
• Emphasis on fermented foods: sauerkraut, kimchi, kefir, yogurt (if tolerated)

Prebiotic Fiber Introduction

Introducing prebiotic fiber too quickly in children with dysbiosis causes gas, bloating, and misery — which leads parents to abandon the effort. The key is to go low and slow.

Start with cooked and cooled starches (resistant starch forms during cooling) — sweet potato, rice, potato. These are gentle and well-tolerated. After 1-2 weeks, add ground flaxseed (half teaspoon daily, mixed into food). Then gradually introduce more diverse sources: cooked leeks, asparagus tips, under-ripe banana, oats.

For children with significant dysbiosis or SIBO, prebiotic fiber may initially worsen symptoms. In these cases, address the overgrowth first, then rebuild with prebiotics after antimicrobial treatment.

Dosing Considerations for Children

Pediatric supplement dosing is not simply “half the adult dose.” Key principles:

• Body weight-based dosing is most accurate for most nutrients
• Fat-soluble vitamins (A, D, E, K) require careful attention to prevent accumulation
• Liquid or powder forms are preferable for children under 6
• Taste matters enormously — the best supplement in the world is useless if the child won’t take it
• Start one supplement at a time — wait 5-7 days before adding another, so you can identify reactions
• Quality is non-negotiable — children’s supplements are rife with artificial colors, sweeteners, and fillers. Choose professional-grade products without dyes, high-fructose corn syrup, or artificial flavors

Putting It Together

The child who presents with constipation, eczema, and behavioral irritability is not three separate problems requiring three separate specialists. That child has a gut that needs attention. The skin is showing you the inflammation. The behavior is showing you the gut-brain axis activation. The constipation is showing you the dysbiosis and dietary mismatch.

Functional medicine sees the whole pattern. Start with the gut. Remove the triggers. Feed the good bacteria. Repair the barrier. Support the terrain.

A child’s microbiome is still being written. Unlike adults, where we’re often trying to rewrite a damaged story, children offer us the chance to shape the narrative from early chapters. Every probiotic drop, every home-cooked meal, every antibiotic we thoughtfully decline or carefully support — these are sentences in a story that will be read for a lifetime.

What story is your child’s gut telling right now — and are you listening?