Beyond the Label: Rethinking IBS & Functional Gut Disorders in Clinical Practice
“I’ve had IBS for 20 years.”
It’s a phrase I hear far too often in clinic. And what’s more worrying is what tends to come next:
“So I just avoid FODMAPs.”
“I don’t eat onion, garlic or legumes.”
“My doctor told me I just have to manage it.”
The problem with a diagnosis like Irritable Bowel Syndrome (IBS) is that it can become a dead-end, both for patients and for practitioners. Rather than a dynamic starting point for further investigation, it’s often used as a final destination - despite the fact that IBS isn’t a disease at all. It’s a syndrome. A collection of symptoms. And the causes underneath? They vary wildly from person to person.
As clinicians, we can (and should) do better.
The Limits of the IBS Label
IBS falls under the broader umbrella of Functional Gastrointestinal Disorders (FGIDs) - conditions defined not by visible pathology, but by gut dysfunction. Alongside IBS, this includes Functional Dyspepsia, Functional Constipation, Functional Diarrhoea, Bloating/Distension Disorders, and more (Drossman, 2016).
Functional Gut Disorders Are Everywhere
If you’ve worked in clinical practice for more than a minute, chances are you’ve encountered someone with Irritable Bowel Syndrome (IBS) or one of the broader Functional Gastrointestinal Disorders (FGIDs). Maybe it’s bloating, constipation, unpredictable diarrhoea, that ever-persistent abdominal discomfort - or the poor soul who has to locate every public toilet before they leave the house.
Globally, FGIDs affect up to 40% of the population, with IBS impacting between 10–20%, depending on which diagnostic criteria you use. Importantly, women are disproportionately affected - some studies suggest up to 70% of IBS diagnoses occur in females, and symptoms are often more severe (Camilleri, 2013).
But here’s the kicker: despite their prevalence, FGIDs are often poorly understood, underdiagnosed, or dismissed altogether. Patients are left navigating restrictive diets, recurring flare-ups, and not-so-helpful advice like "just try to relax” or “go on a low-FODMAP diet”.
How is it Diagnosed?
The Rome IV criteria provide a standardised way to diagnose FGIDs and are especially relevant for IBS. According to Rome IV, IBS is defined as:
Recurrent abdominal pain on average at least 1 day per week in the last 3 months, associated with two or more of the following:
Related to defecation
Associated with a change in stool frequency
Associated with a change in stool form (appearance)
Criteria must be fulfilled for the last 3 months with symptom onset at least 6 months prior to diagnosis (Lacy et al., 2016)
These criteria are helpful, but they can also exclude patients with milder or atypical symptom patterns. Rome IV has been shown to result in a significant drop in IBS diagnoses compared to the older Rome III criteria - particularly in women and non-Western populations (Sperber et al., 2021).
The Mainstream Medical Toolbox: Useful, But Often Incomplete
Conventional approaches to FGIDs typically involve:
Exclusion of red flags (think: weight loss, bleeding, anaemia – this is important and often overlooked!)
Application of Rome IV diagnostic criteria
Pharmaceuticals (e.g., antispasmodics, laxatives, antidepressants)
Dietary advice - typically low FODMAP, gluten-free or elimination-based diets
And while these tools can offer relief, they rarely address the full complexity of the condition - especially when there’s microbial imbalance, food fear, or long-standing dietary restriction involved. Furthermore, the long-term dietary restriction of fermentable fibres (FODMAPs) has been clearly linked with dysbiosis - including reductions in Bifidobacteria and other beneficial taxa - and may carry risks of nutrient deficiencies, particularly if reintroduction phases are not well managed.
Studies confirm:
Reductions in beneficial species, especially Bifidobacteria, during prolonged FODMAP restriction.
SCFA production declines (especially butyrate and acetate).
Potential for nutritional inadequacy, particularly calcium and fibre if not managed by a trained practitioner.
Risk of long-term microbiota shifts opposite to those seen with prebiotic intake.
Let’s Dig Deeper: Key Mechanisms in IBS & FGIDs
1. Visceral Hypersensitivity
IBS patients experience pain and discomfort in response to stimuli that would be benign in most people. This hypersensitivity is likely driven by altered sensory processing in the gut-brain axis, mucosal inflammation, and microbiota changes (Camilleri, 2013).
2. Immune Activation
Post-infectious IBS and mucosal immune cell activation (especially mast cells near enteric nerves) are well-documented in IBS and FD (Barbara et al., 2004).
3. Gut-Brain Axis Dysregulation
Stress, trauma, or dysregulated vagal tone can heighten gut reactivity. For some patients, working on nervous system regulation - including tools like mindfulness, vagal stimulation, and gut-directed hypnotherapy - can be transformative (Palsson et al., 2022).
4. Motility Dysfunction
IBS-C and IBS-D often correspond with slowed or accelerated gut motility. Methane-dominant SIBO, in particular, is linked with constipation due to the motility-slowing effects of methane gas (Pimentel et al., 2003).
5. Altered Gut Microbiota
The microbiome in IBS is distinct from healthy controls - characterised by reduced diversity, lower levels of SCFA-producing species (like Faecalibacterium prausnitzii), increased pathobionts, and dysregulated metabolic activity (Kashyap et al., 2013).
SIBO: The Missed Diagnosis in So Many IBS Patients
Despite its strong link to IBS, Small Intestinal Bacterial Overgrowth (SIBO) is often overlooked. Hydrogen or methane SIBO is present in up to 78% of patients with IBS (Ghoshal et al., 2010).
Symptoms include bloating, flatulence, reflux, altered bowels, and post-meal discomfort - particularly worsened by fermentable foods. Unfortunately, many of these patients are told to remain on long-term FODMAP restriction, which can further compromise microbial diversity and nutritional status over time (Halmos et al., 2014).
If SIBO is present, testing, treating, and rebuilding is crucial to long-term recovery.
A Naturopathic Framework for FGID Care
This is where Naturopathic care shines. In my practice, I take a whole-person approach, working with both the evidence and the individual to unravel the story behind their symptoms.
Advanced Testing
Microbiome profiling using Shotgun Metagenomics testing - MetaXplore (Australia) or TinyHealth (USA)
SIBO breath testing (hydrogen and methane)
Intestinal permeability and mucosal health markers
Personalised Treatment
Herbal antimicrobials (e.g., pomegranate husk, green tea, oregano extract (NOT Essential Oil) when dysbiosis or SIBO is present
Prebiotics, probiotics, and gentle fibre reintroduction
Nervous system regulation and gut-brain therapy – I’ve found the Nerva app to be extremely effective in some patients and it has compelling clinical-trial evidence. (Palsson et al., 2022).
Dietary liberalisation with a focus on diversity and long-term sustainability, slowly and gently of course!
Final Thoughts
IBS is not a dead-end. It’s an invitation to look deeper.
As clinicians, it’s time we move beyond the label and start asking better questions. What’s going on in the microbiome? What’s happening with the gut-brain axis? Has SIBO been ruled out? Is this patient still avoiding onion and garlic 15 years after their diagnosis?
There’s more we can do - and our patients deserve that.
With the right tools and a systems-based view, we can support patients to not just “manage their IBS,” but to heal their gut, rebuild microbial balance, and reclaim food freedom.
I make it my goal to get all of my patients out there to enjoy sharing good wholesome food with their friends and family again.
