Two microbiota subtypes identified in irritable bowel syndrome with distinct responses to the low FODMAP diet

Gut2022 Sep;71(9):1821-1830. doi: 10.1136/gutjnl-2021-325177. Epub 2021 Nov 22.


Kevin Vervier 1Stephen Moss 2 3Nitin Kumar 4Anne Adoum 4Meg Barne 5Hilary Browne 4Arthur Kaser 3 6Christopher J Kiely 7B Anne Neville 4Nina Powell 5Tim Raine 2 8Mark D Stares 4Ana Zhu 4Juan De La Revilla Negro 2Trevor D Lawley 4Miles Parkes 2 3


Author information

1Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK kv4@sanger.ac.uk.

2Department of Gastroenterology, Addenbrookes Hospital, Cambridge, UK.

3Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, Cambridgeshire, UK.

4Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK.

5Department of Dietetics, Addenbrookes Hospital, Cambridge, UK.

6Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, Cambridgeshire, UK.

7Department of Gastroenterology, Royal North Shore Hospital, St Leonards, New South Wales, Australia.

8Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK.


Objective: Reducing FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides and polyols) can be clinically beneficial in IBS but the mechanism is incompletely understood. We aimed to detect microbial signatures that might predict response to the low FODMAP diet and assess whether microbiota compositional and functional shifts could provide insights into its mode of action.

Design: We used metagenomics to determine high-resolution taxonomic and functional profiles of the stool microbiota from IBS cases and household controls (n=56 pairs) on their usual diet. Clinical response and microbiota changes were studied in 41 pairs after 4 weeks on a low FODMAP diet.

Results: Unsupervised analysis of baseline IBS cases pre-diet identified two distinct microbiota profiles, which we refer to as IBSP (pathogenic-like) and IBSH (health-like) subtypes. IBSPmicrobiomes were enriched in Firmicutes and genes for amino acid and carbohydrate metabolism, but depleted in Bacteroidetes species. IBSH microbiomes were similar to controls. On the low FODMAP diet, IBSH and control microbiota were unaffected, but the IBSP signature shifted towards a health-associated microbiome with an increase in Bacteroidetes (p=0.009), a decrease in Firmicutes species (p=0.004) and normalisation of primary metabolic genes. The clinical response to the low FODMAP diet was greater in IBSP subjects compared with IBSH (p=0.02).

Conclusion: 50% of IBS cases manifested a 'pathogenic' gut microbial signature. This shifted towards the healthy profile on the low FODMAP diet; and IBSP cases showed an enhanced clinical responsiveness to the dietary therapy. The effectiveness of FODMAP reduction in IBSP may result from the alterations in gut microbiota and metabolites produced. Microbiota signatures could be useful as biomarkers to guide IBS treatment; and investigating IBSP species and metabolic pathways might yield insights regarding IBS pathogenic mechanisms.



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