Could Your Gut Be Causing Your Pain?

Could Your Gut Be Causing Your Pain? The Fascinating Link Between the Microbiome and Chronic Pain

When we think about chronic pain — whether it’s fibromyalgia, arthritis, migraines or nerve pain — most of us wouldn’t immediately think of our gut. But a growing body of research suggests we probably should.

A new wave of studies is uncovering fascinating connections between the tiny organisms living in our gut (our microbiome) and different types of chronic pain. Could this mean that, one day, your gut test might help pinpoint why you hurt — and even guide treatment?

What Are Researchers Discovering?

Scientists have found what they call “gut microbiome signatures” for various pain conditions. In other words, people with certain chronic pain problems tend to have a distinct balance of gut bacteria compared to those without pain.

Fibromyalgia, complex regional pain syndrome (CRPS), arthritis, migraines and even some kinds of nerve pain are now being linked to these unique gut patterns.

One research team in Israel showed that people with fibromyalgia have a specific microbiome profile that could identify who has the condition — with nearly 90% accuracy. Even more intriguing, when they transplanted gut bacteria from people with fibromyalgia into mice, the mice began to show pain-like behaviours. When they gave the mice healthy bacteria instead, the pain signs disappeared.

In a small pilot study, women with treatment-resistant fibromyalgia who received a gut microbiome transplant from healthy donors reported less pain and fewer symptoms overall.

More recently, the same research team found that people with CRPS — a severe and poorly understood pain condition — had a distinctly different gut microbiome compared to healthy people. These findings were confirmed in patients in both Israel and Canada, suggesting that these gut changes might be reliable no matter where you live.

Could Certain Gut Bacteria Be Protecting Us — or Harming Us?

In CRPS, researchers found higher levels of two bacteria species (Dialister succinatiphilus and Phascolarctobacterium faecium) in people with the condition. On the flip side, three other bacteria (Ligilactobacillus salivarius, Bifidobacterium dentium, and Bifidobacterium adolescentis) were more common in people without CRPS.

Does this mean these bacteria are causing pain or protecting us from it? The honest answer: we don’t fully know yet. But the patterns are strong enough that scientists are taking this connection seriously.

Researchers also measured levels of short-chain fatty acids (SCFAs) in people with CRPS. These compounds, made by healthy gut bacteria when they break down fibre, help keep inflammation in check. People with CRPS had lower levels of SCFAs in their gut and blood — another clue that the gut may play a role in pain.

Testing and Treating: Are We There Yet?

Here’s where things stand today in conventional medicine:
The research is promising — gut bacteria clearly matter for inflammation and pain. We’re seeing possible “signatures” that could help diagnose some pain conditions in the future. But in most standard clinics, gut microbiome testing isn’t yet part of routine pain care — partly because results can be complex and not everyone knows how to translate them into an effective treatment plan.

From a functional medicine perspective, though, it’s a different story.
For nearly two decades, I’ve been using advanced gut testing with my patients — and for many chronic pain conditions, we often start by addressing the gut first. In functional medicine, we know that inflammation, immune function and even pain signalling are deeply influenced by your gut health.

What’s especially exciting now is how far these tests have come in the past 18 years. Testing is more widely available, far more accurate, and can uncover specific imbalances that help us create targeted, practical treatment plans — not just for digestion, but for pain, mood and whole-body wellbeing too.

So while the wider research world still has questions, we already have real tools to test and support your microbiome — and it’s often the best place to begin.

Practical Steps You Can Take Now

A few small studies have found that common probiotics like Lactobacillus, Bifidobacterium, and Saccharomyces boulardii might help ease fibromyalgia symptoms — but not every study has found a benefit, and they’re not a magic fix.

So for now, the best approach is simple and safe:

Eat a fibre-rich, anti-inflammatory diet (lots of plants, whole foods, and fermented foods like yoghurt, kefir, kimchi, or sauerkraut).

Consider a good-quality probiotic if you have digestive issues alongside pain — ideally with guidance.

Work with an experienced practitioner if you want to test or explore targeted gut support.

The Bottom Line

We’re learning more each year about the gut–pain connection. One day, testing your gut bacteria might help diagnose certain pain conditions or guide personalised treatment. Until then, looking after your gut through food, lifestyle and stress management remains one of the best things you can do for your overall health — and it may help ease pain along the way.

If you’re living with chronic pain and wondering if your gut could be part of the puzzle, let’s talk. I’ve been helping patients test, understand and restore their gut health for nearly 20 years — and I’m more excited than ever about what’s possible now.

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