Rebuilding the Microbiome: Where to Start and What Actually Works

Nearly every child we test has a gut microbiome that’s barely functional.

Lactobacillus? Gone.
Bifidobacteria? Gone.
Inflammation? High.
Pathogens? Thriving.
Resilience? Non-existent.

The good news? You can rebuild it. But you have to start at the beginning – and that doesn’t mean throwing probiotics at the problem.

Step One: Fix the Environment

You can’t grow a healthy garden in poisoned soil.

If your child is still exposed to glyphosate-laced food, ultra-processed snacks, artificial sweeteners, and drinking chlorinated tap water, nothing will shift.

– Filter the water.

– Stop buying ultra-processed food.

– Choose organic wherever possible, especially animal-based foods.

– Get outside. Breathe in air that isn’t pumped through a school HVAC system. Touch soil. Interact with the microbial world that actually matters.

Start here. Then move.

Step Two: Feed What You Want to Grow

Starved microbes don’t flourish. And dysbiotic ones will eat whatever’s left – including your gut lining.

At Brainstorm Health, we keep this simple and tailored to the child.

– Animal-based meals with slow carbohydrates like butternut squash or pumpkin.

– Well-cooked, low-oxalate vegetables where tolerated.

– Gelatin-rich broths to support the mucosal layer.

– Fibre isn’t always your friend. If your child’s gut is inflamed or overgrown, fermentable fibres can feed the wrong microbes and make things worse. Forget the “fibre at all costs” rule – it doesn’t apply to every child.

– Prioritise easily digested proteins. Slow-cooked lamb, chicken thighs or turkey mince offer vital building blocks without putting stress on digestion.

– Rotate foods slowly and mindfully. Over-reliance on a narrow set of foods can lead to new sensitivities. Gentle variety helps without overwhelming.

– Keep meals simple. A stressed gut struggles with complexity. Fewer ingredients, eaten in a calm setting, can make all the difference.

This is not about volume. It’s about precision.

Step Three: Identify What’s Blocking Repair

If your child has ongoing gut symptoms, infections, or food reactions, it’s likely they’re dealing with:

– Biofilms

– Mould toxins

– Hidden infections

– Mast cell activation

– Low stomach acid

– Parasites

We run advanced testing when needed. But the clinical picture usually tells us what’s going on. A child constantly bloated after eating, craving sugar, reacting to supplements, or struggling with fatigue is not ready for probiotics yet.

Fix the terrain first.

That might mean:

– Short bursts of targeted antimicrobials

– Mast cell support to calm hyper-reactivity

– Enzymes to support digestion

– Binder support if toxins are at play

– Removing high-histamine foods or oxalates temporarily

 

Step Four: Layer in the Right Support

Once the terrain is safer, we look at rebuilding.

– Saccharomyces boulardii – brilliant during and post-antibiotics, especially when Candida is an issue.

– Soil-based probiotics – used carefully and in rotation.

– Spore-based strains – helpful in some cases, problematic in others.

– Butyrate – as Cal-Mag Butyrate or Sodium Magnesium Butyrate. Key for gut repair and anti-inflammatory signalling.

– GI support formulations — tailored blends to support the lining and mucosal layer.

– Zinc, vitamin A, magnesium, trace minerals — if we want cells to repair, they need raw materials.

– Microimmunotherapy – to help calm chronic inflammation and gently retrain an overactive or depleted immune system.

We don’t give these all at once. We build a protocol based on the child’s symptoms, history, and response.

This isn’t a 30-day reset. It’s a rewiring process.

Step Five: Stop the Cycle

Once you’ve done the work to restore microbial balance, you need to protect it.

– Watch for new antibiotic prescriptions – if necessary, support before, during, and after.

– Continue to support immune resilience – not overstimulation.

– Prioritise nutrient-dense food and rest.

– Avoid reinfection from the environment (mould, parasites, persistent viruses).

– Rethink probiotics – less is often more. Timing and strain matter more than quantity.

Rebuilding the microbiome isn’t about “adding in good bugs”. It’s about removing what’s hostile, creating the right conditions, and giving the body the tools to do what it was designed to do.

It works. But only when you take it step by step.

 

IMPORTANT

The information provided in this article is for educational purposes only and is not a substitute for professional medical advice, diagnosis, or treatment. It is crucial to consult with medical doctors or qualified functional medicine practitioners to address specific health concerns and obtain personalised guidance tailored to individual needs. Never add any supplements to your plan until it has been assessed and approved by your medical doctor or a suitable qualified practitioner who is familiar with your health history. 

Concerned about your child’s health? We’d love to have a chat with you. 

Click the link here to book your Free Discovery Call.