Conditions like Fibromyalgia and Irritable Bowel Syndrome are often treated as entirely separate diagnoses. One sits in the realm of chronic pain and fatigue, the other in digestion. Different specialists, different treatments, different conversations.
As a Registered Nutritionist and Certified Functional Medicine Practitioner specialising in autoimmune conditions, gut health, and chronic symptoms like IBS and fibromyalgia, my role is to look beyond isolated diagnoses and understand how the body is functioning as an interconnected system.
In clinic, I do not treat IBS or fibromyalgia as standalone labels. Instead, I take a root-cause, systems-based approach — exploring the underlying drivers that link digestive symptoms, chronic pain, fatigue, and immune dysregulation.
This includes a detailed investigation into areas such as the gut–brain axis, nervous system regulation, microbiome balance, inflammation, and nutrient status — all of which are central to both IBS and fibromyalgia, yet so often overlooked in conventional care.
This integrative approach is particularly important because many of the clients I work with have been living with IBS symptoms for years before developing more systemic conditions like Fibromyalgia. By the time they reach me, they are often frustrated, having tried multiple diets, protocols, or medications without fully understanding what is driving their symptoms.
Through comprehensive case-taking, functional testing where appropriate, and a highly personalised plan, I work to identify and address the root causes — not just manage symptoms.
This is where a functional medicine approach can be transformative.
Because when you stop viewing the body in silos, and instead understand the connections between gut health, the nervous system, and immune function, you can begin to create meaningful, lasting change.
What does IBS actually mean?
Because, in many cases, it is not a root-cause diagnosis.
It is an umbrella term — a placeholder used when symptoms are present, but the underlying drivers have not yet been fully explored. Bloating, altered bowel habits, discomfort… these are real symptoms, but IBS as a label tells us very little about why they are happening.
And that is where I naturally put my detective hat on.
From a clinical perspective, IBS is often the first signal that something within the gut–brain–immune axis is beginning to dysregulate. It is an early whisper before the body starts speaking more loudly through fatigue, widespread pain, or systemic inflammation — what may later be diagnosed as fibromyalgia.
So rather than seeing these as two separate conditions, I view them as part of a continuum.
What we are often witnessing is not two unrelated diagnoses, but two different expressions of the same underlying imbalances — particularly involving the gut–brain axis, nervous system dysregulation, and immune signalling.
Why symptoms persist (even when you’re doing everything right)
This is why a purely symptom-based approach so often falls short.
If we only manage digestive symptoms, without asking what is driving them, the pattern continues to percolate beneath the surface. Over time, that unresolved dysregulation can extend beyond the gut — influencing pain pathways, energy production, and how the nervous system interprets signals from the body.
And this is often the point at which fibromyalgia enters the conversation. In my clinic, the work is not about separating these conditions into neat categories. It is about connecting the dots between them.
It is about asking:
What triggered this in the first place?
Is there an underlying microbial imbalance or post-infectious shift?
How is the nervous system responding — is it in a constant state of vigilance?
Are there signs of immune activation or barrier dysfunction that have been overlooked?
Because when we start to answer those questions, the picture becomes far clearer — and far more actionable.
The gut–brain axis: more than just digestion
The gut–brain axis is a bidirectional communication network between the gut and the brain, mediated through the nervous system, immune pathways, hormones, and the microbiome.
When this system is functioning well, there is fluid communication. Digestion is efficient, inflammation is regulated, and the nervous system can move between stress and calm with relative ease. But when this axis becomes dysregulated, we begin to see symptoms that extend far beyond the gut.
In IBS, this may present as bloating, altered bowel habits, and visceral hypersensitivity. In fibromyalgia, it may show up as widespread pain, fatigue, and heightened sensitivity to stimuli.
Different symptoms — same underlying conversation within the body.
Nervous system dysregulation
One of the most consistent shared drivers I see is disruption within the autonomic nervous system.
Many individuals with both IBS and fibromyalgia are living in a state of chronic sympathetic activation — what we might loosely call a “fight or flight” bias. Over time, this shifts pain perception, alters gut motility, and impacts how the brain interprets signals from the body.
This is where concepts like central sensitisation become relevant. The nervous system becomes more reactive. Signals are amplified. What might once have been mild discomfort becomes pain, urgency, or fatigue.
And importantly, this is not “in the mind.” It is a physiological shift in how the body processes information.
The role of the microbiome in IBS and fibromyalgia
We also cannot ignore the role of the gut microbiome.
Research now shows that both IBS and fibromyalgia are associated with measurable changes in gut bacteria. Beneficial species such as Bifidobacterium and Faecalibacterium prausnitzii are often reduced, which can impact short-chain fatty acid production, gut barrier integrity, and inflammation.
At the same time, other bacterial groups may become more dominant, influencing pain sensitivity, bile acid metabolism, and immune activation.
Through mechanisms like intestinal permeability, microbial byproducts can interact with the immune system, contributing to low-grade inflammation and altered pain signalling.
This is one of the reasons many people can trace the onset of symptoms back to a trigger — such as a gut infection, antibiotic use, chronic stress, or environmental exposure.
A more integrated (and evidence-based) way forward
A growing body of research supports what I see clinically: IBS and fibromyalgia often share a common underlying physiology.
Studies suggest that up to 50–70% of individuals with Fibromyalgia also experience symptoms of Irritable Bowel Syndrome. This overlap is not incidental — it reflects shared drivers rooted in the gut–brain axis, microbiome, and nervous system.
When we look more closely at the microbiome, we can begin to see why this connection exists. For example, one of the most important bacteria I often assess in clinic is Faecalibacterium prausnitzii. This is a key butyrate-producing species, meaning it helps generate short-chain fatty acids that support the integrity of the gut lining and regulate inflammation.
In many individuals with IBS and fibromyalgia, levels of Faecalibacterium prausnitzii are reduced. This matters because lower butyrate production can compromise the gut barrier, increase intestinal permeability, and contribute to low-grade inflammation — all of which can influence pain signalling and nervous system sensitivity.
In simple terms, when this type of bacteria is depleted, the gut becomes more vulnerable, and the ripple effect can extend far beyond digestion.
From a clinical perspective, this is where a more investigative approach becomes essential.
Rather than relying on broad labels, I use comprehensive stool testing to assess microbial balance, inflammation, digestive function, and gut integrity. This allows us to understand what is actually happening beneath the surface — and, importantly, what to do about it.
If you would like to explore this in more detail, you can find further information about the stool test I use in clinic here: Comprehensive Stool Test (GI Effects)
The important nuance
Not every case will look the same. For some, the gut is the primary driver. For others, it is the nervous system. And for many, it is a feedback loop between the two.
But what remains consistent is that these conditions rarely exist in isolation.
Bringing it together
The overlap between fibromyalgia and IBS is not coincidental. It reflects a deeper, more interconnected picture of how the body is responding to stress, inflammation, and dysregulation.
When we understand that, we move away from fragmented care and towards something far more cohesive — and ultimately, far more effective.
Because the goal is not simply to quiet symptoms. It is to restore communication within the body so that those symptoms no longer need to be there in the first place.
If you are struggling with IBS, fibromyalgia, or ongoing symptoms that do not seem to make sense — and you are ready to understand what is actually driving them — I have created a free guide to help you get started.
You can download The Autoimmune Recovery Plan here: Download The Autoimmunity Recovery Plan
This guide walks you through the key root causes I look at in clinic — and the first steps you can take to begin supporting your gut, nervous system, and immune health in a more targeted, effective way.
FAQs
Can IBS cause fibromyalgia?
IBS does not directly cause fibromyalgia, but both conditions often share underlying drivers such as gut dysbiosis, nervous system dysregulation, and inflammation.
Why do IBS and fibromyalgia occur together?
They are both linked through the gut–brain axis, meaning imbalances in gut health can influence pain sensitivity, fatigue, and nervous system function.Can improving gut health help fibromyalgia?
In many cases, supporting the gut microbiome, reducing inflammation, and regulating the nervous system can help improve symptoms.
Can improving gut health help fibromyalgia?
In many cases, supporting the gut microbiome, reducing inflammation, and regulating the nervous system can help improve symptoms.
References;
- Garofalo C, Cristiani CM, Ilari S, Passacatini LC, Malafoglia V, Viglietto G, Maiuolo J, Oppedisano F, Palma E, Tomino C, Raffaeli W, Mollace V, Muscoli C. Fibromyalgia and Irritable Bowel Syndrome Interaction: A Possible Role for Gut Microbiota and Gut-Brain Axis. Biomedicines. 2023 Jun 13;11(6):1701. doi: 10.3390/biomedicines11061701. PMID: 37371796; PMCID: PMC10296515.
VJ Hamilton, BSc, RNT
VJ Hamilton is a Registered Nutritionist (BANT) and an expert in autoimmune disease. VJ combines her knowledge from her medical science degree in Biochemistry & Immunology with Nutritional Therapy to offer a thorough and personalised approach to support her clients based on the most current scientific research. VJ runs a virtual and in-person nutritional therapy and functional medicine practice, The Autoimmunity Nutritionist, specialising in gut skin and immune health.