Faecal Microbiota Composition and Metabolomic Profiles as Diagnostic Markers in Patients with Irritable Bowel Syndrome: A Review

Abstract

Irritable bowel syndrome is diagnosed on symptoms alone, and a confirmatory test has been sought for two decades. Faecal microbiota and metabolite profiles differ reproducibly between patients and controls. Whether that difference is large enough to diagnose an individual is a separate question, and the answer so far is no. Objectives: To review the published evidence on faecal microbiota composition and metabolomic profiling as diagnostic markers in irritable bowel syndrome: which taxa and metabolites differ consistently, what accuracy classifiers based on them achieve, and how they compare with the one faecal test already in routine use. Material and Methods: Narrative review of case-control cohorts, meta-analyses, metabolomic profiling studies and diagnostic guidelines indexed in PubMed and the major gastroenterology journals. Studies were eligible if they reported differences in faecal microbiota or metabolites between patients with irritable bowel syndrome and comparators, or the diagnostic accuracy of a marker or classifier built from them. No new patient data were generated; every estimate quoted is one published by the original investigators.
Results: Pooling 13 studies covering 360 patients and 268 controls, three taxa were consistently reduced: Bifidobacterium (standardised mean difference -1.17), Faecalibacterium prausnitzii (-1.05) and Lactobacillus (-0.85), with the reduction most marked in diarrhoea-predominant disease. Bacteroides-Prevotella and Escherichia coli did not differ. A faecal volatile metabolite model separated diarrhoea-predominant disease from Crohn's disease, ulcerative colitis and healthy controls with sensitivities of 94, 96 and 90 per cent and specificities of 82, 80 and 80 per cent. Combining microbial and metabolite profiling in a single Bayesian classifier achieved 84 per cent overall accuracy and 86 per cent for diarrhoea-predominant disease in cross-validation. By comparison, faecal calprotectin distinguishes inflammatory bowel disease from irritable bowel syndrome with pooled sensitivity of 85.8 per cent and specificity of 91.7 per cent across 17 studies and 1,956 patients. Conclusion: Microbiota and metabolite differences in irritable bowel syndrome are real and reproducible at group level, and the reported classifier accuracies come from cross-validation within derivation cohorts rather than independent testing. The one faecal marker with established diagnostic utility remains calprotectin, which excludes an alternative diagnosis rather than confirming this one. Abbreviations: IBS – Irritable Bowel Syndrome, IBS-D – Diarrhoea-Predominant IBS, IBS-C – Constipation-Predominant IBS, IBS-M – Mixed-Type IBS, IBD – Inflammatory Bowel Disease, SCFA – Short-Chain Fatty Acid, VOC – Volatile Organic Compound, SMD – Standardised Mean Difference, NMR – Nuclear Magnetic Resonance, PLS-DA – Partial Least Squares Discriminant Analysis, AUC – Area Under the Receiver Operating Characteristic Curve.