How the Gut Microbiome Shapes Your Child’s Health and Behavior

Your Child's Microbes; Your Parenting Allies

Your child’s digestive system is home to a vast community of tiny organisms called microbes. Together, they form the gut microbiome, a living ecosystem that influences everything from digestion and immunity to sleep, focus, metabolism, and mood.

You can think of the gut microbiome like a veggie garden. Your plants will grow strong and steady if you nourish them well, but opportunistic weeds will take over when there’s too much space or not enough nourishment. When the garden is tended and fed well, everything stays balanced. 

The same is true in your child’s gut: balance creates resilience.

How a Child’s Microbiome Is Formed

A child’s microbiome begins developing long before the first bite of food. 

As early as in utero, microbes from mom may be kickstarting a child's microbiome. Studies are still inconclusive about how the microbiome of the fetus may be impacted by the maternal microbiome, but it's possible that mom's microbes may influence what her baby inherits even before birth.

Even if it turns out the fetus isn't impacted directly by mom's microbes, the birth process is certainly a time when we do inherit microbes from our mothers. A vaginal birth coats the baby in the mother’s beneficial microbes, forming the foundation of the infant’s gut community. Cesarean birth introduces a different set of microbes from the hospital environment, which may delay the growth of certain helpful bacteria.

Antibiotics given to mom during labor or to the baby early in life can reduce key microbes like Bifidobacteria and Lactobacillus, which are vital for digestion, brain development, and immune balance. These need to be replenished.

Breastmilk is nature’s way of rebuilding and enriching the microbiome. Human milk is alive! It contains both prebiotics (food for gut bugs) and probiotics (the bacteria themselves), which feed and grow helpful microbes. Babies who are breastfed tend to have higher levels of Bifidobacteria and a reduced risk of developing childhood conditions like asthma, eczema, and ADHD.

As children continue to grow, their early environment, experiences, and diet continue to shape the gut ecosystem. Stress, trauma, illness, and medications (including GERD medications, laxatives and steroids) can narrow the range of microbes, while outdoor play, social connection, and a diverse diet expand it.

Current thinking is that around age three the microbiome should begin to resemble that of an adult, but it continues to shift in response to diet, sleep, and stress well beyond that.

So that's how we got here. But as I'm always telling parents, the only reason to look back is to figure out how we got here so we can find our next best move. Once we know how your child’s gut story began, we can help write the next chapter more intentionally.

The Fleet of Helpful Microbes

Helpful microbes form the backbone of your child’s gut community. They are our “parenting allies”; when they are working well, everything is easier. They digest food, create nutrients, and help the body and brain communicate; they break down fibre, produce short-chain fatty acids that calm inflammation, train the immune system, support neurotransmitters like serotonin and dopamine, regulate metabolism, create GABA and vitamins, and protect against irritation from less helpful species. 

Can you see why I call them our parenting allies? When these microbes are robust, your child gets sick less often and gets better more quickly. They have less tummy pain, more energy, and feel more comfortable. Their toxic load and inflammation are lower, and the gut-brain connection is strengthened.

This is why I harp on helping parents support good gut health in their kids.

Let’s look at some of these helpers….

Bifidobacteria

Among the earliest and most important residents of the infant gut, Bifidobacteria digest complex carbohydrates and create short-chain fatty acids that protect the gut lining. Children with higher Bifidobacteria tend to have stronger digestion and more balanced immune systems. Bifidobacteria also play a role in reducing gut hyperpermeability, which is critical for preventing systemic inflammation.

Lactobacillus

Found mainly in the small intestine, Lactobacillus species digest sugars, make lactic acid to keep the gut balanced, and support immune tolerance. They also help reduce inflammation and help crowd out opportunistic microbes by creating an environment that’s less hospitable to them.

Akkermansia muciniphila

These microbes live near the gut lining and help maintain the mucus layer that protects the intestines. Balanced levels strengthen the barrier and regulate immune responses. Low levels of Akkermansia have been associated with metabolic issues like obesity and insulin resistance, whereas high levels are associated with inflammation and gut-lining issues.

Faecalibacterium, Roseburia, and Blautia

These species create butyrate, a fatty acid that fuels the colon and supports the gut-brain connection. Butyrate also has systemic anti-inflammatory effects, which can benefit conditions like eczema, asthma, and even anxiety. Low levels of these are linked to inflammation and mood issues.

Together, these helpful species keep the gut calm and flowing, and the brain well-nourished. When they thrive, your child is more likely to experience steady energy, balanced moods, and strong immune resilience.

The Opportunistic or Less Helpful Microbes

Every gut also houses a smaller group of microbes that can become disruptive when they take up too much space. When stress, illness, antibiotics, or dietary changes reduce the helpful microbes, these opportunists grow quickly. In excess, they produce gases and toxins that irritate the gut and affect mood, focus, and energy.

Some opportunistic species have been linked with specific childhood concerns:

• Candida albicans: is associated with fatigue, eczema, and irritability when overgrown. Candida thrives in high-sugar environments, so reducing refined sugars is a key strategy for keeping it in check. It also tends to thrive during and after a course of antibiotics.
  
  

• Klebsiella: is linked with inflammatory bowel disease and certain joint conditions. Klebsiella overgrowth can also contribute to gut lining problems and may exacerbate systemic inflammation.
  
  

• Desulfovibrio: these produce hydrogen sulfide that can inflame the gut. It has been found in higher amounts in some children with autism spectrum disorders. Desulfovibrio tends to flourish in low-fiber, high-fat diets.
  
  

• Bilophila wadsworthia: these tend to increase with high-fat, low-fibre diets and contribute to gut inflammation. Bilophila is particularly sensitive to dietary shifts, so even small changes in fibre intake can make a big difference here.
  
  

• Methanobrevibacter smithii: these archaea produce methane gas that can slow digestion and cause constipation.
  
  

• Clostridium perfringens: can release toxins that can lead to diarrhea and make mood instability and focus problems worse. 
  
  

• Enterococcus: these are part of the normal gut microbiome and play useful roles in digestion and immune signalling. But when the gut environment is inflamed and out of balance, certain Enterococcus species can trigger inflammation, release toxins, and contribute to urinary tract or systemic infections. We wouldn't want to eliminate this family entirely, but we do want them to be in balance with other helpful microbes, which we can do by supporting digestion, supporting beneficial Bifidobacteria and Lactobacillus, and reducing sugar and processed foods.

These opportunistic species flourish when the gut environment is out of balance. The goal isn’t necessarily to destroy them completely but to restore harmony so the entire ecosystem functions smoothly.

What About Parasites?

Parasites are larger organisms that can live in the gut alongside bacteria and yeast. They thrive in microbiomes that are low in stomach acid, digestive enzymes, and beneficial bacteria, and high in inflammation or undigested food. 

When the gut lining is weak or digestion is sluggish, parasites can settle in and avoid the immune system. Not every parasite causes trouble, but they can steal nutrients, irritate the gut wall, and trigger immune reactions that show up as fatigue, mood changes, or skin issues. 

A diverse, well-fed microbiome and strong digestion make the gut far less welcoming to these guests.

So, a child’s gut is shaped by birth, early experiences, daily habits, and even the microbes in other family members. Helpful microbes build stability, while opportunistic ones step in when the system is stressed or undernourished. Understanding both groups lays the foundation for restoring balance and helping your child’s body and brain thrive.

Why Things Get Out of Balance

A healthy microbiome is like a small, self-sustaining city. When traffic flows, supplies arrive, and everyone does their job, things stay calm and balanced. But when the roads are blocked by stress, poor diet, illness, or certain medications, certain microbes lose their food supply while others take advantage of the disruption.

That’s how opportunistic species begin to grow and crowd out the helpers.

Over time, this imbalance can change the messages that flow between the gut, brain, and immune systems, which makes it harder for a child to regulate.

Aside from maternal health and birth method that were already mentioned, here are some more common reasons a child's microbiome can fall out of balance…

1. Too Little Fibre and Color  - Without enough of this, populations of helpful microbes shrink. Studies show that children who eat a wide variety of plant foods have stronger, more diverse microbiomes, while low-fibre, highly processed diets allow inflammatory species to flourish.

2. Too Much Sugar - sugar feeds microbes like Candida and certain strains of Enterococcus which produce by-products that irritate the gut lining and trigger cravings for even more sugar.

3. Antibiotics, Some Medications, and Chemicals - Medications like antibiotics, antacids, mood medications, NSAIDs, and antihistamines are sometimes essential, but they clear out helpful microbes and open up a window of opportunity for opportunistic species to multiply faster than the helpful ones can return. Some also disrupt the gut barrier and reduce stomach acid, making it easier for unhelpful microbes to thrive. Early antibiotic use has been linked to lower microbial diversity and a greater risk of mood, skin, immune and digestive challenges later in childhood.

4. Low Stomach Acid and Slow Digestion - When stomach acid is low or bile flow is weak, food isn’t fully broken down. Over time, this can lead to bloating, gas, or discomfort after meals. 

5. Environmental Toxins and Hidden Triggers - Everyday chemicals in plastics, cleaning products, and even tap water can shift the gut’s microbial balance. While it’s impossible to avoid all toxins, small changes help: use filtered water, store food in glass containers, and choose whole foods with fewer additives to reduce the body’s overall toxic burden.

The Impact of Stress and Trauma, on the Microbiome

Stress and trauma are among the most powerful and least recognized forces shaping a child’s microbiome. Stress hormones like cortisol and adrenaline change how food moves through the intestines, lower stomach acid, and alter bile flow. This stress reduces butyrate-producing Faecalibacterium and Roseburia, and increases inflammatory species like Desulfovibrio and Bilophila. Beneficial species that create serotonin and GABA continue to be crowded out, and a child descends into a vicious cycle: 

• Stress shifts the microbiome toward inflammation.
  

• Inflammation and altered gut signalling feed back to the brain, keeping the child more reactive or anxious.
  

• The heightened stress further stresses the gut and weakens digestion.

• Opportunistic microbes perpetuate inflammation and further crowd out the beneficial microbes that create GABA and serotonin (which we need to modulate stress).

• More stress builds, which creates more inflammation

On and on it goes.... In children who have experienced stress and trauma early in life, this loop can become deeply embedded, increasing vulnerability to anxiety and immune dysregulation later on.

How to Bring Balance Back

Once we understand that the gut is a living ecosystem shaped by food, stress, sleep, and emotion, the next question becomes: what needs attention first?

A good functional stool test looks at several key areas:

• Digestive capacity: Is your child breaking down fats, carbohydrates, and proteins properly? Are stomach acid, enzymes, and bile doing their jobs so nutrients can be fully extracted from food?
  

• Microbial balance: Are there enough of the helpful species like Bifidobacteria, Lactobacillus, and Faecalibacterium? Are opportunistic bacteria or yeasts like Candida or Klebsiella taking up too much space?
  

• Inflammation: Are there markers showing irritation or an overactive immune response?
  

• Gut barrier strength: Are the intestinal cells strong and well-connected, or is the barrier letting irritants leak through?
  

• Metabolites: What are the microbes doing in there? Are they creating GABA, Vitamins, Histamine, fatty acids, and Methane (to name a few)?
  
  

This information helps clarify where to start. For example:

• If the gut is inflamed, the first step may be to soothe and calm with anti-inflammatory nutrients and remove irritants.
  

• If digestion is weak, we may want to rebuild digestive capacity by supporting stomach acid, bile flow, and enzymes.
  

• If helpful microbes are low, focusing on re-seeding and re-feeding them with fibre, prebiotics, and targeted probiotics may be the place to focus
  

• If opportunistic microbes or yeasts are high, we may want to crowd them out with diet changes, herbal antimicrobials, probiotics, or botanical blends.
  

• If the gut lining is damaged, we may want to rebuild and nourish it with nutrients and soothing herbs that repair the barrier.
  
  

No gut test is perfect or diagnostic, but it can shine a light on where to focus so we don’t push the wrong system at the wrong time.

As balance returns, you’ll often see small but meaningful shifts - steadier moods, fewer tummy aches, better focus, improved sleep, stronger immune resilience, and a calmer nervous system.

Why Bother With Gut Health?

Whether you do a gut test or not, keep this in mind: resilience isn’t about chasing every symptom or microbe. It’s about understanding the story the body is telling and responding with the right kind of care.

A microbiome test helps decode that story so you can see where to begin and what your child’s body needs most right now. But even without testing, simple steps like improving diet, reducing stress, improving sleep, and supporting digestion can have profound effects on gut health.

Understanding the gut sets the stable foundation children need to grow, learn, and feel safe from the inside out.

Related articles:

https://www.jesssherman.com/blog/child-digestion-support-tips

https://www.jesssherman.com/blog/microbiome-testing-for-kids-benefits

https://www.jesssherman.com/blog/types-of-gluten-testing-for-kids

https://www.jesssherman.com/blog/teen-anxiety-is-it-nutritional

https://www.jesssherman.com/blog/types-of-probitoics-for-kids

Select References

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Rastogi, S., & Singh, R. (2022). Frontiers in Pharmacology. Lactobacillus species, gut balance and inflammation.

Amin Abbasi, et al. (2023). Probiotics and Antimicrobial Proteins. Akkermansia muciniphila 

Nature Communications (2024). Fiber diversity and microbiome resilience.

Science Translational Medicine (2016). Antibiotics, birth mode and diet in early life and gut diversity.

Cell Mol Gastroenterol Hepatol. (2022). Klebsiella and gut inflammation.

J Affect Discord (2023). Early life trauma and gut microbiome later in life

M. Bio (2020) Caregiving behaviors and the child gut microbiome

Nature Microbiology (2017). Desulfovibrio and autism-related gut imbalance.

Nature Microbiology (2019). Early-life stress and gut-brain interaction.

Cell Host & Microbe (2015). Bilophila wadsworthia and diet.

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Frontiers in Psychiatry (2022). Stress, microbiome, and mood regulation.

Brain, Behavior, and Immunity (2021). Chronic stress and microbial imbalance.

Environmental Health Perspectives (2019). Chemical exposure and microbial balance.