Microbiome Testing for Kids: When to Do It and How It Helps (video)
Click the PLAY button to hear me describe the two microbiome stool tests I use with kids and why.
Looking for a gut assessment for your kids? Contact us to discuss options.
Here's the low-down....
If your child is dealing with gut issues, anxiety, ADHD, skin flare-ups, or frequent illnesses and you’re looking for a natural solution beyond medications, this post is for you.
Microbiome testing offers insight into what’s happening in your child’s gut. And since the gut influences everything from digestion to immune health to mood and focus, it can be a powerful place to start.
The stool test I use with families isn’t a diagnostic tool; it doesn’t screen for disease or condition. Instead, it gives a snapshot of the gut ecosystem, helping parents see what might be out of balance and what may help their kids feel better from the inside out.
What Is Microbiome Testing in Kids?
A microbiome test for kids starts with a simple stool sample you collect at home and send to a lab. The lab analyzes the sample and gives you a report outlining what microbes are present, how they’re behaving, and what they're producing..
Here’s the key, though: a child’s microbiome is not just a smaller version of an adult’s. Kids, and their microbiomes, are still developing. Their microbiome reflects their age, birth method, diet, environment, and immune development.
So, interpreting a stool test through an adult lens can lead to confusion and unnecessary interventions.
We must adapt our view of the microbiome to the reality of developing kids.
Why We Can't Use Adult Gut Guidelines for Kids' Guts
Here are three things that worry me when practitioners and parents read a microbiome test for a child without adjusting to the reality of childhood.
1. Misunderstanding Diversity and "Missing" Beneficials
In an adult gut, low microbial diversity is a red flag for dysbiosis or reduced resilience. In kids though, lower diversity may be a normal part of microbial development. Their microbiome is still maturing.
When it comes to diversity, a toddler’s microbiome will look different from a 6-year-old’s, which will look different from an adolescent’s. And trying to “correct” this risks disrupting the natural progression.
Applying pediatric reference ranges to understand diversity, and focusing on helping parents foster a food and lifestyle environment that champions microbial maturation, is often the best approach.
2. Over-treating Commensal Overgrowths or Opportunists
The presence of a species doesn’t always mean it's causing a problem. Certain microbes flagged in an adult's test can be concerning, while in kids they may be transient.
What matters is the full picture: What symptoms are they experiencing? Have they recently been sick or exposed to a virus? Did they just have a round of antibiotics?
Health history and overall patterns are what to look for in the developing microbiome of a child. Often with kids, restoring balance through prebiotic support, polyphenol-rich foods, and nourishment is more helpful than going after specific microbes with a “kill” strategy.
3. Misreading Inflammatory Markers
Markers like calprotectin or SIgA can fluctuate a lot in children. Elevated IgA, for example, may just reflect teething or recent exposure to illness at school. Using adult thresholds can lead to unnecessary worry and potentially overpathologizing normal immune activity, especially in younger kids whose mucosal immunity is still calibrating.
The pediatric immune system has its own rhythm. Again, context matters. Symptoms, age, recent illness or exposure - the entire health picture, along with age-appropriate norms need to be considered when reading a stool test for a child.
What I Look For in a Child’s Gut Test
Rather than chasing single organisms, I look for the following patterns in the microbiome of kids:
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Sufficiency: Are key beneficial microbes present in age-appropriate amounts?
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Overgrowth: Are certain microbes gaining too much ground due to low resilience or recent stressors? Can we push them out, or do we need to be more aggressive?
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Inflammation: Is there evidence of inflammation and immune system activation? What is the context? Is there any evidence the gut lining is compromised?
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Digestion: Is the child breaking down and absorbing food efficiently?
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Metabolite activity: Are microbes producing things like short-chain fatty acids, GABA, vitamins, or histamine?
- Signature Patterns: Has the child fallen into a microbial patterns that predisposes them to developing common childhood health concerns like eczema, sleep issues, food allergy, diabetes, immune vulnerability, anxiety, or obesity?
Attending to these patterns helps us create an age-appropriate plan.
When Should You Consider a Microbiome Test for Your Child?
“Can’t we just eat healthy and see what happens?” Absolutely! And for many kids, that’s enough. But if symptoms persist despite doing the best you can with diet, or if you want to know that things are optimized, gathering data through a gut test can offer clarity and direction.
Microbiome Assessments are especially helpful if your child has:
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Chronic constipation, diarrhea, belly pain, or bloating
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Eczema, rashes, or frequent skin flare-ups
- Picky eating that's not responding to conventional strategies
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Ongoing mood or behavior concerns (anxiety, ADHD, anger/rage)
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A history of repeated infections or antibiotics
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Trouble maintaining a healthy weight
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A family history of autoimmune or mental health conditions
Gut tests can offer a proactive look at gut health. But results should always be interpreted through a pediatric lens.
How Microbiome Testing Helps
Once you have test results, you can move from guessing to strategy. A good test can help you understand:
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Which probiotic or prebiotic strains might actually help
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What foods to prioritize or reduce for now
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Whether there’s gut inflammation or poor digestion
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How the gut may be affecting mood, immunity, or focus
Bonus: many kids love seeing their “gut bug” report. It can give them a sense of ownership and curiosity, which makes new habits easier to try.
What Makes a Good Microbiome Test for Kids?
Not all stool tests are designed with children in mind. The ones I prefer:
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Use age-specific reference ranges
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Apply shotgun metagenomics technology (this gives a broader picture than tests that only look for specific microbes and is now the gold standard for microbiome assessment tools)
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Include digestive and immune function markers
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Measure microbial metabolites like short-chain fatty acids, histamine, and GABA production
- Include "signature patterns" - microbial patterns that predispose a person to developing certain health issues (like eczema, sleep issues, food allergy, diabetes, or obesity)
These features give you a more complete picture and a better chance of meaningful next steps.
Final Thoughts
The gut plays a central role in children’s health, from digestion and nutrient absorption to immune regulation and even brain function.
If you’re feeling stuck or simply want a clearer picture of what’s going on inside, microbiome testing for kids can be a powerful tool, as long as it’s interpreted with care.
A child's microbiome is a living system, still under construction. Applying adult templates to pediatric data can result in unnecessary worry and missed opportunities.
When reviewing a stool test for a child, parents and practitioners should pause and ask:
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Is this expected for their developmental stage?
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Am I seeing true dysfunction or just immaturity?
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Is there clinical correlation to the findings?
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Could supporting rather than suppressing be the better path here?
Working with kids’ gut health requires a different lens. And when we adjust our expectations to match the biology of a developing system, our support becomes more precise, more respectful of the child’s natural trajectory, and often, more effective.
Looking for a gut assessment for your kids? Contact us to discuss options.
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3 Things Every Parent Needs to Know About the Gut-Brain Connection
