How a Healthy Gut Microbiome May Support Neuroplastic Pain, Fibromyalgia and ME/CFS

Chronic pain and fatigue conditions such as neuroplastic (nociplastic) pain, fibromyalgia, and ME/CFS are increasingly understood as disorders of nervous system regulation, immune signalling, and energy metabolism — not simply problems within muscles or joints.

One area of growing interest is the gut microbiome: the trillions of bacteria, viruses, and fungi living in the digestive tract. While research is still evolving, there is a strong and biologically plausible case that supporting a healthy microbiome may play a meaningful role in symptom management.

Understanding Neuroplastic Pain, Fibromyalgia and ME/CFS

These conditions share several core features:

• Central sensitisation – an overactive nervous system that amplifies pain and sensory signals

• Immune dysregulation and low-grade inflammation

• Autonomic nervous system imbalance (fight-or-flight dominance)

• Fatigue, brain fog, sleep disturbance and gut symptoms

Crucially, this does not mean symptoms are “all in the mind”. It means the brain, nerves, immune system and metabolism are interacting differently — and the gut sits at the centre of that interaction.

The Gut–Brain–Immune Axis

The gut communicates constantly with the brain and immune system via:

• The vagus nerve

• Immune signalling molecules (cytokines)

• Microbial metabolites such as short-chain fatty acids (SCFAs)

• Hormones and neurotransmitters (including serotonin and GABA)

A disrupted microbiome (dysbiosis) can increase intestinal permeability (“leaky gut”), allowing inflammatory signals to circulate — potentially fueling pain sensitisation and fatigue.

Why the Microbiome Matters in Neuroplastic Pain

Neuroplastic or nociplastic pain arises when pain pathways become over-learned and hyper-reactive, even in the absence of ongoing tissue damage.

A healthy microbiome may help by:

• Reducing neuroinflammation

• Supporting vagal tone, helping the nervous system shift out of threat mode

• Producing SCFAs (especially butyrate) that help regulate microglial activation in the brain

• Influencing neurotransmitters involved in pain modulation

Animal models consistently show that altering the gut microbiome can increase or reduce pain sensitivity — one of the strongest signals in this field.

Fibromyalgia and the Microbiome

People with fibromyalgia frequently report:

• IBS-type symptoms

• Food sensitivities

• Bloating and altered bowel habits

Research has identified distinct differences in gut bacterial composition in fibromyalgia compared with healthy controls. While this does not yet prove causation, it supports the idea that the microbiome may be involved in:

• Pain amplification

• Fatigue

• Cognitive symptoms (“fibro fog”)

Small human studies (including dietary and microbiome-targeted interventions) suggest symptom improvements are possible, but larger, better-controlled trials are still needed.

ME/CFS, Energy Metabolism and the Gut

ME/CFS is characterised by:

• Profound fatigue

• Post-exertional symptom exacerbation

• Immune and autonomic dysfunction

The microbiome may be relevant through its effects on:

• Mitochondrial function and energy production

• Immune balance

• Gut barrier integrity and endotoxin exposure

Several studies show reduced microbial diversity and altered metabolic outputs in ME/CFS. Again, this doesn’t yet mean the microbiome is the cause — but it may be a modifiable contributor.

What Does the Evidence Say Overall?

Strength of evidence by area:

• Biological plausibility: Strong

• Animal and mechanistic studies: Strong

• Human observational studies: Moderate

• Human intervention trials (diet, probiotics, FMT): Early and mixed

In other words:
👉 Promising, sensible to support — but not a standalone cure.

Supporting a Healthy Microbiome (Safely)

For people with chronic pain and fatigue, the goal is gentle support, not aggressive intervention.

Helpful strategies may include:

• A diverse, fibre-rich, anti-inflammatory diet (as tolerated)

• Polyphenol-rich foods (berries, olive oil, herbs, colourful plants)

• Identifying and addressing individual food intolerances

• Supporting gut regularity and digestive comfort

• Cautious, personalised use of prebiotics or probiotics

• Avoiding unnecessary restriction, which can reduce microbial diversity

Any intervention should be paced and personalised, particularly in ME/CFS where symptom flares can occur.

The Take-Home Message

A healthy microbiome won’t “switch off” neuroplastic pain, fibromyalgia or ME/CFS on its own — but it may:

• Lower inflammatory load

• Improve nervous system regulation

• Support energy metabolism

• Enhance resilience to stressors

As part of a whole-person, systems-based approach, microbiome support is a low-risk, potentially high-impact foundation for many people living with chronic pain and fatigue.