Module 21

Microbiome Disruptors Checklist

Identify and eliminate the factors actively destroying your child's gut ecosystem

Building a healthy microbiome isn't just about adding good things — you also have to stop doing the things that are actively killing the beneficial bacteria. Many common, everyday exposures devastate gut diversity. Check how many apply to your child and prioritize eliminating the ones you can control.

Antibiotic Exposure

More than 2 courses of antibiotics in the past year— A single course of antibiotics can reduce gut diversity by 30% and take 6-12 months to recover. Some species never return.

Antibiotics prescribed without confirming bacterial infection— Most ear infections and upper respiratory infections are viral. Antibiotics do nothing for viruses but still destroy gut bacteria.

Broad-spectrum antibiotics used when narrow-spectrum would work— Amoxicillin-clavulanate (Augmentin) destroys far more gut flora than amoxicillin alone. Ask your doctor if narrow-spectrum is an option.

No probiotic supplementation during or after antibiotics— Saccharomyces boulardii during antibiotics (it's yeast — antibiotics don't kill it) + multi-strain probiotic for 1-3 months after.

Antibiotics given in first 6 months of life— The most vulnerable period. Early antibiotics are associated with increased risk of asthma, allergies, obesity, and autoimmune conditions.

Dietary Disruptors

High sugar intake (juice, candy, sweetened snacks, flavored yogurt)— Sugar feeds pathogenic bacteria (Candida, Clostridium) at the expense of beneficial species. Flavored yogurt has 12-18g added sugar — negating much of the probiotic benefit.

Processed/ultra-processed foods make up >50% of diet— Emulsifiers (polysorbate 80, carboxymethylcellulose), artificial sweeteners, and preservatives directly damage the gut lining and reduce microbial diversity.

Low fiber intake (fewer than 3 servings fruits/vegetables per day)— Gut bacteria eat fiber. Without it, they eat the mucus lining of the gut instead, increasing intestinal permeability.

Artificial sweeteners (sucralose, aspartame, acesulfame-K)— Sucralose reduces beneficial gut bacteria by up to 50% in animal studies. Found in "sugar-free" drinks, gum, and many "healthy" kids' products.

Low diversity diet (same 10-15 foods on rotation)— Microbial diversity mirrors dietary diversity. The more different plant foods your child eats, the more diverse their gut ecosystem.

Excessive dairy (more than 24 oz milk per day)— Crowds out other foods, reduces iron absorption, and limits dietary diversity. Stick to 16-20 oz for toddlers.

Water & Environmental Disruptors

Drinking unfiltered municipal (chlorinated) water— Chlorine is a disinfectant — it kills bacteria. That includes the beneficial bacteria in your child's gut. Use a carbon filter at minimum.

Regular exposure to antibacterial soap or hand sanitizer— Triclosan (now banned in soap but still in some products) and alcohol-based sanitizers alter skin and gut microbiomes. Regular soap and water is sufficient.

Conventional (non-organic) produce without washing— Pesticide residues (especially glyphosate) are antimicrobial — they kill soil bacteria and gut bacteria alike.

Living in a bleach-heavy cleaning environment— Homes using bleach-based cleaners weekly have children with higher rates of respiratory infections. Switch to vinegar, hydrogen peroxide, or microfiber.

Limited outdoor/nature exposure— Children who play in soil, gardens, forests have significantly more diverse microbiomes. Dirt isn't the enemy — sterility is.

No pets in the home— Children raised with dogs have more diverse microbiomes and lower rates of allergies and asthma. Not a reason to get a dog — but don't keep kids away from animals out of germ fear.

Medical & Other Disruptors

Proton pump inhibitors (PPIs) for reflux— Reduce stomach acid, allowing pathogenic bacteria to survive passage to the gut. Increases C. difficile risk. Use only when truly needed.

NSAIDs used frequently (ibuprofen)— Can increase intestinal permeability ("leaky gut") with chronic use. Occasional use is fine.

C-section birth without probiotic intervention— C-section babies miss vaginal microbe transfer. Consider vaginal seeding (discuss with provider) or early probiotic supplementation (B. infantis).

Exclusively formula-fed without probiotic supplementation— Formula lacks the 200+ HMOs that selectively feed beneficial bacteria. Supplementing with B. infantis partially compensates.

Chronic stress (family conflict, school pressure, screen overuse)— Cortisol directly alters gut motility and microbiome composition. The gut-brain axis runs both directions.

Your Disruptor Score

Count the items you checked above.

Checked Items	Assessment	Priority Action
0-3	Low disruption	Focus on adding more probiotic and prebiotic foods. Your foundation is solid.
4-7	Moderate disruption	Address the top 2-3 items you checked. Filter water, reduce processed foods, add fermented foods daily.
8-12	High disruption	The microbiome is under significant stress. Start probiotic supplement, filter water, overhaul snack foods, and limit unnecessary antibiotics.
13+	Critical disruption	Major intervention needed. Work with a functional medicine practitioner. Consider comprehensive stool testing. Prioritize dietary overhaul and environmental cleanup.

You don't have to fix everything at once. The three highest-impact changes: (1) filter your drinking water, (2) replace one processed snack per day with a whole food, and (3) add one fermented food daily. That's a meaningful shift in 90 days.