Dysbiosis and relapse-related microbiome in inflammatory bowel disease : a shotgun metagenomic approach
Serrano-Gómez, Gerard (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Mayorga, Luis (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Oyarzun, Iñigo (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Roca, Joaquim (Consejo Superior de Investigaciones Científicas (Espanya))
Borruel, Natalia (Hospital Universitari Vall d'Hebron)
Casellas, Francesc (Hospital Universitari Vall d'Hebron)
Varela, Encarna (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Pozuelo, Marta (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Machiels, Kathleen (Translational Research Center for Gastrointestinal Disorders, Leuven, Belgium)
Guarner, Francisco (Hospital Universitari Vall d'Hebron. Institut de Recerca)
Vermeire, Severine (University Hospitals Leuven (Bèlgica))
Manichanh, Chaysavanh (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas)
Universitat Autònoma de Barcelona

Date:	2021
Abstract:	Crohn's disease (CD) and ulcerative colitis (UC), the two main forms of inflammatory bowel disease (IBD), affect several million people worldwide. CD and UC are characterized by periods of clinical remission and relapse. Although IBD patients present chronic alterations of the gut microbiome, called dysbiosis, little attention has been devoted to the relapse-related microbiome. To address this gap, we generated shotgun metagenomic data from the stools of two European cohorts-134 Spanish (followed up for one year) and 49 Belgian (followed up for 6 months) subjects-to characterize the microbial taxonomic and metabolic profiles present. To assess the predictive value of microbiome data, we added the taxonomic profiles generated from a previous study of 130 Americans. Our results revealed that CD was more dysbiotic than UC compared to healthy controls (HC) and that strategies for energy extraction and propionate production were different in CD compared to UC and HC. Remarkably, CD and UC relapses were not associated with alpha- or beta-diversity, or with a dysbiotic score. However, CD relapse was linked to alterations at the species and metabolic pathway levels, including those involved in propionate production. The random forest method using taxonomic profiles allowed the prediction of CD vs. non-CD with an AUC = 0. 938, UC vs. HC with an AUC = 0. 646, and CD relapse vs. remission with an AUC = 0. 769. Our study validates previous taxonomic findings, points to different relapse-related growth and defence mechanisms in CD compared to UC and HC and provides biomarkers to discriminate IBD subtypes and predict disease activity.
Grants:	Instituto de Salud Carlos III PI17/00614 Instituto de Salud Carlos III PI20/00130
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, i la comunicació pública de l'obra, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original. No es permet la creació d'obres derivades.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Crohn's disease ; Ulcerative colitis ; Flare ; Shotgun metagenomics
Published in:	Computational and Structural Biotechnology Journal, Vol. 19 (december 2021) , p. 6481-6489, ISSN 2001-0370

DOI: 10.1016/j.csbj.2021.11.037
PMID: 34938418

9 p, 2.1 MB

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