Integrated microbiota and metabolite profiles link Crohn’s disease to sulfur metabolism

Amira Metwaly, Andreas Dunkel, Nadine Waldschmitt, Abilash Chakravarthy Durai Raj, Ilias Lagkouvardos, Ana Maria Corraliza, Aida Mayorgas, Margarita Martinez-Medina, Sinah Reiter, Michael Schloter, Thomas Hofmann, Matthieu Allez, Julian Panes, Azucena Salas and Dirk Haller ()
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Amira Metwaly: Chair of Nutrition and Immunology, Technical University of Munich
Andreas Dunkel: Leibniz-Institute for Food Systems Biology, Technical University of Munich
Nadine Waldschmitt: Chair of Nutrition and Immunology, Technical University of Munich
Abilash Chakravarthy Durai Raj: Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis
Ilias Lagkouvardos: ZIEL Institute for Food and Health, Technical University of Munich
Ana Maria Corraliza: Inflammatory Bowel Disease Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd
Aida Mayorgas: Inflammatory Bowel Disease Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd
Margarita Martinez-Medina: Laboratory of Molecular Microbiology, Department of Biology, Universitat de Girona
Sinah Reiter: Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich
Michael Schloter: Helmholtz Zentrum München, German Research Center for Environmental Health, Research Unit Comparative Microbiome Analysis
Thomas Hofmann: Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich
Matthieu Allez: APHP, Hôpital Saint Louis, Department of Gastroenterology, INSERM UMRS 1160, Paris Diderot, Sorbonne Paris-Cité University
Julian Panes: Inflammatory Bowel Disease Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd
Azucena Salas: Inflammatory Bowel Disease Unit, Hospital Clínic de Barcelona, IDIBAPS, CIBERehd
Dirk Haller: Chair of Nutrition and Immunology, Technical University of Munich

Nature Communications, 2020, vol. 11, issue 1, 1-15

Abstract: Abstract Gut microbial and metabolite alterations have been linked to the pathogenesis of inflammatory bowel diseases. Here we perform a multi-omics microbiome and metabolite analysis of a longitudinal cohort of Crohn’s disease patients undergoing autologous hematopoietic stem cell transplantation, and investigational therapy that induces drug free remission in a subset of patients. Via comparison of patients who responded and maintained remission, responded but experienced disease relapse and patients who did not respond to therapy, we identify shared functional signatures that correlate with disease activity despite the variability of gut microbiota profiles at taxonomic level. These signatures reflect the disease state when transferred to gnotobiotic mice. Taken together, the integration of microbiome and metabolite profiles from human cohort and mice improves the predictive modelling of disease outcome, and allows the identification of a network of bacteria-metabolite interactions involving sulfur metabolism as a key mechanism linked to disease activity in Crohn’s disease.

Date: 2020
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DOI: 10.1038/s41467-020-17956-1

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