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Irritable bowel syndrome diagnosis: the practitioner’s guide
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How can you refine the diagnosis of irritable bowel syndrome? Dr Balon-Perin guides the practitioner towards a personalised approach.
Irritable bowel syndrome (IBS) remains one of the most common diagnoses in consultation, and also one of the most frustrating for the practitioner.
Between abdominal pain, bloating, alternating diarrhoea and constipation, and the emotional toll, the causes look both multiple and diffuse.
Yet, as Dr Balon-Perin shows in the Simplycure webinar “How can we measure irritable bowel syndrome through the microbiota?”, recent progress in metagenomics is finally making these imbalances easier to understand and to document objectively.
Studying the gut microbiota thus becomes a key tool for refining the diagnosis, guiding care and telling patient profiles apart more accurately.
Visceral hypersensitivity: the key to irritable bowel syndrome
IBS rests above all on visceral hypersensitivity: an exaggerated response of the enteric nervous system to stimuli that are sometimes minimal1.
Dr Balon-Perin reminds us that this heightened sensitivity is fed by three interdependent mechanisms:
a micro-inflammation of the intestinal mucosa, linked to an unbalanced microbiota;
an excessive fermentation, responsible for distension and pain;
and a hyper-reactivity of mast cells, which releases histamine and inflammatory mediators.
These interactions create a genuine vicious circle: inflammation, gas, pain, then stress and nervous dysregulation heighten visceral sensitivity further still.
In other words, IBS is not “all in the head”: it reflects a broken dialogue between the microbiota, the mucosa and the enteric nervous system.
The role of the microbiota in diagnosing irritable bowel syndrome
The gut microbiota acts as a true immunometabolic organ. When its balance breaks down, it becomes one of the earliest markers of the condition2.
Dr Balon-Perin distinguishes two broad families of bacteria:
the pro-inflammatory ones, needed for immune vigilance but harmful in excess;
and the protective ones, which produce butyrate and keep the mucosa healthy.
A drop in bacterial diversity (dysbiosis) disrupts this symbiosis: the mucosal barrier thins, intestinal permeability rises and pain signalling intensifies.
For the practitioner, this view changes the paradigm: it is no longer only about identifying a functional disorder, but about documenting measurable imbalances through microbiota analysis.
Clinical picture: telling the two main types of imbalance apart
According to Dr Balon-Perin, these two main types of microbial imbalance therefore call for opposite approaches.
Dysbiosis profileMicrobial featuresDominant symptomsTherapeutic directionInflammatoryExcess E. coli, Klebsiella, Proteus; low Faecalibacterium prausnitzii and bifidobacteria3Diffuse pain, fatigue, irregular bowel habit, sometimes anxietyMucosal support, probiotics, omega-3, a diet rich in prebiotic fibreFermentativeExcess of H₂ or H₂S-producing bacteria (Dorea, Desulfovibrio…)Bloating, flatulence, alternating diarrhoea/constipationLow-FODMAP diet, sulphur restriction, targeted antimicrobial herbal medicine
This table draws on the clinical cases of Luc (inflammatory profile) and Gérald (fermentative profile) presented in the webinar, illustrating the value of individualised diagnosis.
Luc presented with an inflammatory dysbiosis, with a shortfall in protective bacteria and immune over-activity. The therapeutic strategy aimed to restore the mucosa: a diet rich in fibre, prebiotics, probiotics and omega-3.
Gérald, by contrast, had a fermentative dysbiosis: an excess of H₂S-producing bacteria was destroying mucus and driving painful hypersensitivity. He improved with a low-FODMAP diet, a restriction of sulphur-containing foods and targeted herbal medicine (oregano, berberine).
This pair of cases underlines how important it is not to stop at the symptom, but to measure the microbiota in order to understand the true nature of the imbalance.
Metagenomics: a revolution in diagnosis
One of the webinar’s major contributions concerns investigative methods.
Conventional faecal culture methods only manage to grow a fraction of the microbiota, because most anaerobic bacteria do not survive exposure to oxygen4.
Metagenomics gets around this obstacle through bacterial DNA sequencing.
This technique, set out in detail by Dr Balon-Perin, provides precise mapping:
it identifies the species present, whether beneficial or pathogenic;
it measures their relative proportions;
and it allows these profiles to be correlated with clinical symptoms.
One technical detail makes all the difference: the sample must be placed in a tube containing a DNA stabiliser immediately after collection, otherwise the results are biased.
The clinical value is twofold: documenting the imbalance (inflammatory, fermentative or mixed), and guiding the therapeutic strategy without trial and error.
Fermentation, SIBO, SIFO: when the flora runs wild
In some patients, fermentation takes over.
Bacteria migrate towards the small intestine, causing bacterial overgrowth (SIBO) or fungal overgrowth (SIFO).
According to the studies cited by Dr Balon-Perin, these imbalances may be present in close to two thirds of patients with IBS.
The gases produced (hydrogen, methane, hydrogen sulphide) explain the typical distension and pain.
H₂-predominant SIBO tends to be associated with diarrhoea;
CH₄-predominant SIBO tends towards constipation;
and excess H₂S weakens the mucosa and worsens post-prandial pain.
As for intestinal candidiasis, it is not confined to severe immunosuppression: it also appears in stressed or tired patients, on antibiotics or proton pump inhibitors5.
The urinary D-arabinitol test proves particularly useful for picking up this often silent fungal overgrowth.
An integrative approach to diagnosing irritable bowel syndrome
Beyond the microbiota, Dr Balon-Perin underlines the role of stress and of nervous regulation.
Emotions influence mucosal permeability, mucus secretion and digestive motility via the vagus nerve.
Here too, microbiota analysis sheds light on the interaction: certain bacterial imbalances contribute to neuroinflammation and modulate serotonin production, worsening bowel and mood disturbances.
This integrative view reconciles physiology, microbiology and psychology: stress is not an isolated cause, but an amplifier of a disturbed microbial terrain.
Giving the IBS diagnosis meaning again
Every patient arrives with the same complaint: “My stomach hurts, but nobody can find anything.”
What Dr Balon-Perin shows is that we can, at last, “find something”.
Behind diffuse pain, bloating or altered bowel habit there often lie measurable microbial imbalances: inflammatory, fermentative or mixed.
Metagenomic analysis makes them visible, explains why some patients react badly to FODMAPs, others to stress or to particular fermentation patterns, and lets the therapeutic response be matched to each person’s real profile.
And perhaps, seen through this lens, it gives meaning back to symptoms once thought “functional”, which above all reflect a physiology in search of balance.
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