Microbiome Medicine & the Gut-Brain Axis

Microbiome medicine and the gut-brain axis

The health of your gut microbiome shapes your brain, mood, immune system, energy and overall health. Microbiome medicine is the part of our integrative approach that assesses and treats the gut-brain-immune axis — using advanced testing to find dysbiosis, inflammation and the specific microbial imbalances that drive symptoms far beyond the gut, then repairing and rebalancing it with a structured “remove, repair, restore” programme. For the complex, multi-system conditions we treat, it is one of the highest-yield interventions available.

What microbiome medicine is

Microbiome medicine treats the gut as a central organ of whole-body health rather than just a digestive tube. When there is an imbalance in the gut, it can contribute to a wide variety of symptoms outside the gut — from mood and anxiety problems and behavioural disturbances to chronic fatigue, brain fog, autoimmunity, difficulty clearing infections and even neurodegenerative changes. That is because gut bacteria and other microbes, such as yeasts, moulds and protozoa, produce chemicals that can change our neurotransmitter production and have a direct effect on brain and energy function.

By identifying the specific imbalances, we can treat to restore optimal function and improve symptoms that seem unrelated to the gut at first glance — including mental health, fatigue, pain and autoimmunity. This is rarely considered as part of standard care despite a large and growing evidence base, and for our patients it is one of the most impactful places to start.

The gut-brain-immune axis

The gut communicates constantly with the brain and immune system through the vagus nerve and a web of chemical messengers. An estimated 90% of the body’s serotonin, along with significant amounts of dopamine and GABA — our primary calming neurotransmitter — is made in the gut, and specific bacteria metabolise glutamate and produce GABA. So the balance of the microbiome directly shapes mood, anxiety, focus and sleep.

When the gut is inflamed or dysbiotic, or the gut barrier becomes permeable (“leaky gut”), microbial by-products and inflammatory signals reach the bloodstream and brain, driving neuroinflammation, sensory sensitivity, fatigue and mood symptoms — and, in conditions such as MCAS, feeding an over-reactive immune system. This is why treating the gut so often improves symptoms that appear to have nothing to do with digestion.

What we test for

What we find

We use advanced testing — a comprehensive stool analysis, often combined with urine metabolic testing of microbial by-products — to assess the gut-brain-immune axis. This can reveal:

• Overgrowth of pathogenic bacteria, SIBO and methanogen overgrowth
• Fungal and yeast overgrowth, including mould-illness markers
• Reduced intestinal barrier function (“leaky gut”)
• Maldigestion and malabsorption
• Markers of micro-inflammation and immune suppression
• Specific bacterial toxins and metabolite imbalances that impair neurotransmitter and energy production, and chronic opportunistic infections

What we commonly see work

These findings turn a vague “gut problem” into specific, treatable targets — and let us track change over time as the gut is repaired.

Remove, repair, restore

Treating the gut well requires a structured sequence, not a single probiotic. Our approach follows a remove, repair, restore process, tailored to what testing reveals:

• Remove — reduce overgrowths of pathogenic bacteria, yeast, fungus or SIBO, and remove the dietary and environmental triggers feeding them. Order matters: fungal overgrowth and SIBO usually need addressing before gut-lining repair will hold.
• Repair — heal the gut barrier and reduce inflammation using targeted nutrients such as slow-release glutamine and short-chain fatty acids, alongside an anti-inflammatory therapeutic diet.
• Restore — rebuild a resilient, balanced microbiome with specific probiotics and potent botanicals, and support ongoing motility and digestion.

Because our patients are often very sensitive, protocols are introduced carefully and paced, and evolve over time as biomarkers and symptoms improve — allowing a gradual reduction while maintaining the gains.

Therapeutic diets and nutraceuticals

Diet is inseparable from microbiome medicine, but there is no single gut diet that suits everyone. Depending on the person and their test results, we may use different types of diets — such as specific anti-inflammatory diets with temporary removal of immunogenic food proteins, low-histamine diets where mast-cell features are present, a low-FODMAP diet while we clear a methanogen overgrowth, a specific carbohydrate diet for low-grade inflammatory bowel, and many more — all personalised to the person and their biochemistry. In children, sensory-aware “food chaining” expands the diet without mealtime battles.

Alongside diet, clinical-grade nutraceuticals are chosen for synergistic effect — because glutamine and probiotics help repair the gut lining, but not if fungal overgrowth and SIBO have not been addressed first. This is why microbiome medicine sits within a wider functional medicine plan and is often combined with nervous system regulation, since the gut and the nervous system are in constant two-way conversation.

The conditions microbiome medicine helps

Because the gut sits at the centre of so many symptoms, microbiome medicine underpins our treatment of:

• MCAS, mould illness and IBS and digestive conditions
• Chronic fatigue/ME, long covid and fibromyalgia
• Anxiety, depression and OCD
• Neurodivergence — troublesome symptoms in people with ADHD, autism and AuDHD (we are not trying to cure autism; we help with the symptoms that cause distress — see our neurodivergence hub)
• EDS and chronic pain, where gut inflammation amplifies symptoms

Frequently asked questions

It is the assessment and treatment of the gut microbiome and gut-brain-immune axis — using advanced stool and urine testing to find dysbiosis, overgrowths, leaky gut and inflammation, then treating them with a structured “remove, repair, restore” programme of targeted probiotics, botanicals, therapeutic diets and gut-barrier repair.

Yes. The gut makes most of the body’s serotonin and much of its dopamine and GABA, and gut microbes produce chemicals that affect brain and energy function. An imbalanced gut can drive anxiety, low mood, brain fog, fatigue, pain and autoimmunity — often with few obvious gut symptoms.

Rarely. A single probiotic seldom fixes a dysbiotic gut, and order matters — fungal overgrowth and SIBO usually need addressing before gut-lining repair will hold. That is why we follow a structured, tested “remove, repair, restore” sequence tailored to you.

Yes — the London Resilience Clinic offers microbiome and functional medicine as part of an integrative approach, led by Dr Dani Gordon, with particular expertise in complex, multi-system and neurodivergent presentations.

Microbiome medicine, delivered by specialist doctors

• Test, don’t guess. Comprehensive stool and urine testing turns a vague “gut problem” into specific, treatable targets.
• A structured sequence. Remove, repair, restore — in the right order, paced for sensitive patients.
• Whole-body thinking. We treat the gut to improve mood, energy, pain and immunity, not just digestion.
• Part of one integrated plan. Stacked with functional medicine, nutrition, nervous system regulation and medication for a synergistic effect.