The Gut–Brain Axis in Kids: How Tummy Troubles Affect Mood and Behaviour

It started with tummy aches after lunch.

Jasper, a bright and curious 7-year-old, came to see me because he was struggling with stomach pain, restless sleep, and frequent emotional outbursts that seemed to come from nowhere. His mum said, “He’s always been a little sensitive, but lately, he’s either flat or flying off the handle.” She’d tried removing gluten, cutting down on screen time, even magnesium baths — nothing seemed to help.

When we began exploring deeper, a story started to unfold: one of gut imbalances quietly shaping his mood, behaviour, and resilience. It’s something I see often — and it starts in the gut.

What Is the Gut–Brain Axis?

The gut and brain are in constant communication through a complex network of nerves, hormones and chemical messengers. This is what we call the gut–brain axis — a two-way system linking digestion, immunity, and emotional health.

In children, this connection is still developing. Their nervous systems are more sensitive, their gut microbiome still evolving, and they often lack the language to describe discomfort. Instead, they show us through mood swings, tantrums, clinginess, poor sleep, or changes in appetite.

When a child’s gut is out of balance, it can affect their:

• Focus and concentration

• Mood regulation

• Energy and motivation

• Sleep rhythms

• Immune system

• Ability to cope with stress

Signs the Gut–Brain Axis Might Be Out of Balance

Every child is different, but here are some patterns I often see:

• Ongoing tummy aches, constipation or loose stools

• Behaviour that’s easily dysregulated – such as outbursts, anxiety or withdrawal

• Night waking, bedwetting or restless sleep

• Cravings for sugar or carbs

• Food intolerances, skin rashes or eczema

• Frequent illness or slow recovery from viruses

• Clinginess, separation anxiety or low mood

• A history of antibiotics or reflux medications

Parents will often say, “He’s just not himself,” or “She gets overwhelmed so easily.”

Why Gut Health Matters So Much in Childhood

The gut isn’t just about digestion — it’s a foundational system that helps regulate:

• Neurotransmitters like serotonin and GABA (which calm the nervous system)

• The immune system (up to 70% of it lives in the gut!)

• Inflammation and nutrient absorption

• Detoxification and hormone balance

When the gut is inflamed or imbalanced (a state called dysbiosis), it can disrupt how the brain receives signals. In kids, this can look like frequent meltdowns, a short fuse, or a child who’s often anxious or low — especially after eating certain foods.

How I Support the Gut–Brain Axis Naturopathically

When I work with children, I take a whole-child approach. No two cases are the same, but here’s what I often explore:

1. Gut Microbiome Testing (like Co-Biome or similar)

If there’s a long history of gut issues, antibiotics, or behavioural concerns, a stool test can be incredibly helpful to see:

• Beneficial vs. harmful bacteria

• Signs of inflammation or leaky gut

• Parasites or yeast overgrowth

• Levels of short-chain fatty acids (linked to mood and immune health)

2. Herbal and Nutritional Remedies

Gentle, evidence-informed options might include:

• Slippery elm or marshmallow root for soothing the gut lining

• Chamomile or lemon balm for calming nerves and digestion

• Zinc, magnesium, and B-vitamins for mood and nervous system balance

• Probiotics (including SB) tailored to their presentation

3. Homeopathic Support

For children who are highly sensitive, easily overwhelmed, or stuck in stress response, I often prescribe homeopathic remedies such as:

• Nux vomica – if tension and irritability are linked to gut upset

• Lycopodium – for performance anxiety with bloating and gas

• Chamomilla – for children who are inconsolable and reactive with tummy pain

4. Food-as-Medicine

We gently explore:

• Reducing high-histamine or gut-irritating foods (like excessive dairy, sugar, preservatives)

• Adding gut-loving foods like broth, simple ferments (if tolerated), and fibre

• Working within the family’s rhythm — no restrictive diets, just small, supportive shifts

Rhythms That Restore

Alongside remedies, simple lifestyle rhythms make a powerful difference. These are some I often recommend:

• Consistent mealtimes to support blood sugar and circadian balance

• Calm bedtime routines with magnesium baths or storytime

• Outdoor movement to regulate nervous and digestive systems

• Screen-free meals to promote mindful eating and better digestion

• Family connection time (even 10 minutes a day) to anchor their nervous system

Clinic Snapshot

Jasper's case became a beautiful example of what’s possible with gentle, whole-body care. After a few weeks on a personalised plan with gut-soothing herbs, a tailored probiotic, and a homeopathic remedy for his emotional reactivity, his mum emailed me:
"The tummy aches are nearly gone, and he’s not snapping as much. He told me yesterday, ‘I feel better in my tummy and my heart.’"

Sometimes it’s the smallest things that show us healing is happening.

A Gentle Word

If your child is struggling with their tummy, their mood, or both — you are not imagining the link. The gut–brain connection is real, and there are gentle, natural ways to bring things back into balance. You’re not alone on this path.

Ready to Support Your Child’s Gut–Brain Health?

If you’re curious about how naturopathy might support your child’s mood, behaviour or digestion, I’d love to help.

Book a Children’s Naturopathy Consultation

Let’s gently bring their spark back together.

With warmth and care,
Ayelet x