Rebuilding the Gut Microbiome in Children with IBD

When I review stool tests from children with IBD, the same pattern shows up again and again.

The friendly, anti-inflammatory bacteria that should be thriving - like Bifidobacteria, Faecalibacterium prausnitzii, and Akkermansia - are often drastically reduced, or even missing altogether.

In their place?

I often see higher levels of troublemakers like E. coli, Enterococcus, or Ruminococcus gnavus - species known to stir up inflammation. The protective mucus layer is often thinner, digestion feels "off", and the immune system is on high alert.

This kind of imbalance doesn’t happen overnight, and it can’t be reversed overnight either. But the amazing news is - the gut can recover when we rebuild it in the right order, step by step.

When we rebuild the gut microbiome in children with IBD, the goal isn't to add in dozens of supplements - it's to restore balance step-by-step, creating a calmer environment where healthy bacteria can take root again.

Here's how I approach microbiome rebuilding in children with IBD - gently, logically, and with long-term resilience in mind.

1. Build the Foundations to Rebuild the Gut Microbiome in Children with IBD

Create an environment where good bacteria can thrive.

Before we add in probiotics or special foods, we need to prepare the gut — like tending the soil before planting a garden. The terrain has to be right for healthy bacteria to take root.

• Dial down ultra-processed foods.

  Children’s guts are especially sensitive to emulsifiers, preservatives, and artificial sweeteners in packaged snacks and drinks. These can weaken the gut barrier and feed the wrong bacteria.

  Try swapping one processed snack for a while-food option each week - those small, steady changes really add up.

• Filter the water.

  Chlorine and other residues in tap water can irritate an inflamed gut. A simple water filter can make a real difference to daily gut comfort.

• Choose organic where you can.

  Pesticides like glyphosate can disrupt microbial balance in the same way antibiotics do. Prioritise organic for animal products and the “dirty dozen” fruits and veg — even partial swaps help.

• Get outdoors.

  Soil, grass, pets, and fresh air all expose your child to diverse microbes that help train the immune system. Let them dig, garden, or walk barefoot — nature truly is part of the gut-healing toolkit.

  
  

Once the gut’s environment feels calmer and “cleaner,” it’s ready for the next step.

Outdoor play helps children reconnect with nature - a simple, natural way to support microbial diversity and gut health.

2. Support and Soothe Digestion

Nourish the gut without overwhelming it

Children with IBD often have fragile digestion, especially during or after a flare. The goal here is to calm inflammation and provide the raw materials for repair - without overloading the system.

Try these gentle strategies:

• Start soft. Swap raw, fibrous foods with cooked, low-fibre vegetables like zucchini, pumpkin, and carrots.

• Keep meals simple. Pair quality proteins (chicken, white fish, lamb) with soothing carbs like rice or well-cooked squash.

• Include soothing broths. Gelatine and amino acids from bone broth support the gut lining and reduce inflammation – just be careful if your child has histamine sensitivity and prepare alternative short cook or vegetable broths instead.

• Be flexible with fibre. During active inflammation, a low-residue approach can ease symptoms. As healing progresses, gently reintroduce soluble fibre - one new source at a time - to feed beneficial bacteria and encourage butyrate production.

• Prioritise variety and protein. Growing bodies need plenty of building blocks for tissue repair.

If your child is following a medical or therapeutic diet (like the SCD - Specific Carbohydrate Diet, IBD-AID or CDED), always check changes with your practitioner - these diets can be powerful but need careful balancing.

Once digestion feels calmer, we can check for anything still blocking full recovery.

Gentle, soothing meals like soups and broths can calm inflammation and support gut healing during IBD recovery.

3. Identify and Clear What’s in the Way

Sometimes deeper imbalances keep the gut stuck.

Even with a great diet, some children don't progress because hidden disruptors are in play - things like:

• Bacterial or yeast overgrowths (including SIBO or C. difficile)

• Biofilms that shelter harmful microbes

• Low stomach acid or enzyme output

• Mast cell overactivity (causing histamine reactions)

• Environmental mould or toxin exposure

• Undiagnosed parasites

These can all fuel ongoing inflammation and prevent repair. Common clues include bloating, pain after meals, sugar cravings, or poor response to probiotics.

Addressing these “road blocks” can involve:

• Targeted antimicrobials or antifungals (herbal or prescribed)

• Digestive support such as enzymes or gentle acid aids

• Mast cell calming nutrients (quercetin, vitamin C, DAO enzyme)

• Toxin binders under supervision if mould exposure is suspected

Think of this phase as weeding the garden - clearing what’s harmful so healthy microbes can flourish again.

If you’d like to explore whether overgrowths or infections could be playing a role, contact me for testing options.

4. Rebuild and Reseed

Once the gut is calm, it’s ready to be replenished.

Now comes the fun part - helping beneficial microbes and gut cells bounce back. But remember: slow and steady wins here. More is not better, precision is everything.

A few key players to consider:

• Saccharomyces boulardii a gentle probiotic yeast shown to support immune balance and reduce IBD relapses.

• Spore-based probiotics like Bacillus coagulans - resilient species that can safely restore diversity.

• Evidence-based bacterial strains. E. coli Nissle 1917, Bifidobacterium longum, and Lactobacillus rhamnosus GG are among the best studied in Crohn's and colitis.

• Feed beneficial bacteria. If fibre is tolerated, use gentle prebiotics like PHGG or GOS. If not, butyrate supplements can directly nourish colon cells.

• Repair the gut lining. Nutrients such as L-glutamine, N-acetyl-glucosamine, zinc carnosine, and demulcent herbs (slippery elm, marshmallow) strengthen the barrier.

• Replete key nutrients. Vitamin D, zinc, iron, B12, and magnesium are essential for immune balance and mucosal repair — but should be tested before supplementing.

Every child's tolerance is different - go gently, and work with your practitioner to guide the pace.

5. Maintain and Protect

Keep the progress going.

Once your child’s gut feels more stable, the focus shifts to resilience - keeping inflammation low and preventing regressions.

• Be antibiotic-wise. Avoid unnecessary use, and always support the gut if antibiotics are required.

• Prioritise rest and play. Adequate sleep, downtime, and physical activity all reduce gut inflammation.

• Stick to real, varied foods. Natural colours and polyphenols from fruits and vegetables feed beneficial microbes.

• Address triggers early. Keep an eye out for damp/mould exposure, oral health issues, or food reactions.

• Use probiotics intentionally. High doses aren’t needed indefinitely - save targeted strains for stressful periods or after antibiotics.

Children's microbiomes are always changing as they grow. Coming back to these steps every so often helps keep the gut balanced and inflammation-free.

The Takeaway

Rebuilding your child's microbiome with IBD isn't about quick fixes - it's about doing things in the right sequence:

1️⃣ Clean the terrain

2️⃣ Soothe and stabilise digestion

3️⃣ Remove deeper blocks

4️⃣ Rebuild carefully

5️⃣ Protect what’s been rebuilt

When we follow this rhythm, we create lasting, meaningful change.

If you’d like to meet some of the key microbes that live in your child’s gut, head over to my Meet the Microbes hub.

Important: This information is for educational purposes only and not a substitute for medical advice. Always consult your child’s gastroenterologist or qualified practitioner before making any dietary or supplement changes.

If you’d like to understand what your child's microbiome looks like right now - or you'd like help designing a step-by-step rebuilding plan get in touch here - I’d be happy to guide and support you.