Combinatorial, additive and dose-dependent drug-microbiome associations.

Sofia K Forslund, Rima Chakaroun, Maria Zimmermann-Kogadeeva, Lajos Markó, Judith Aron-Wisnewsky, Trine Nielsen, Lucas Moitinho-Silva, Thomas S B Schmidt, Gwen Falony, Sara Vieira-Silva, Solia Adriouch, Renato J Alves, Karen Assmann, Jean-Philippe Bastard, Till Birkner, Robert Caesar, Julien Chilloux, Luis Pedro Coelho, Leopold Fezeu, Nathalie Galleron, Gerard Helft, Richard Isnard, Boyang Ji, Michael Kuhn, Emmanuelle Le Chatelier, Antonis Myridakis, Lisa Olsson, Nicolas Pons, Edi Prifti, Benoit Quinquis, Hugo Roume, Joe-Elie Salem, Nataliya Sokolovska, Valentina Tremaroli, Mireia Valles-Colomer, Christian Lewinter, Nadja B Søndertoft, Helle Krogh Pedersen, Tue H Hansen, Jens Peter Gøtze, Lars Køber, Henrik Vestergaard, Torben Hansen, Jean-Daniel Zucker, Serge Hercberg, Jean-Michel Oppert, Ivica Letunic, Jens Nielsen, Fredrik Bäckhed, S Dusko Ehrlich, Marc-Emmanuel Dumas, Jeroen Raes, Oluf Pedersen, Karine Clément, Michael Stumvoll, Peer Bork

Journal: Nature 2022;600(7889):500-505

PMID: 34880489

Abstract

During the transition from a healthy state to cardiometabolic disease, patients become heavily medicated, which leads to an increasingly aberrant gut microbiome and serum metabolome, and complicates biomarker discovery. Here, through integrated multi-omics analyses of 2,173 European residents from the MetaCardis cohort, we show that the explanatory power of drugs for the variability in both host and gut microbiome features exceeds that of disease. We quantify inferred effects of single medications, their combinations as well as additive effects, and show that the latter shift the metabolome and microbiome towards a healthier state, exemplified in synergistic reduction in serum atherogenic lipoproteins by statins combined with aspirin, or enrichment of intestinal Roseburia by diuretic agents combined with beta-blockers. Several antibiotics exhibit a quantitative relationship between the number of courses prescribed and progression towards a microbiome state that is associated with the severity of cardiometabolic disease. We also report a relationship between cardiometabolic drug dosage, improvement in clinical markers and microbiome composition, supporting direct drug effects. Taken together, our computational framework and resulting resources enable the disentanglement of the effects of drugs and disease on host and microbiome features in multimedicated individuals. Furthermore, the robust signatures identified using our framework provide new hypotheses for drug-host-microbiome interactions in cardiometabolic disease.

© 2021. The Author(s), under exclusive licence to Springer Nature Limited.

Address: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.; Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany.; Charité-Universitätsmedizin Berlin, Berlin, Germany.; Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin and the Max-Delbrück Center, Berlin, Germany.; Berlin Institute of Health (BIH), Berlin, Germany.; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany.; Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.; Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany.; Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin and the Max-Delbrück Center, Berlin, Germany.; Berlin Institute of Health (BIH), Berlin, Germany.; Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, INSERM, Paris, France.; Nutrition Department, Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Paris, France.; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.; Center for Microbiology, VIB, and Rega Institute, KU Leuven, Leuven, Belgium.; Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, INSERM, Paris, France.; Assistance Publique Hôpitaux de Paris, UF Biomarqueurs Inflammatoires et Métaboliques, Biochemistry and Hormonology Department, Tenon Hospital, Paris, France.; Centre de Recherche Saint-Antoine, Sorbonne Université, INSERM UMR S938, Paris, France.; Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany.; Charité-Universitätsmedizin Berlin, Berlin, Germany.; Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, Gothenburg, Sweden.; Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK.; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Shanghai, China.; Nutritional Epidemiology Research Team (EREN), Sorbonne Paris Cité Epidemiology and Statistics Research Centre (CRESS), U1153 INSERM, U1125, INRA, CNAM, University of Paris 13, Paris, France.; Metagenopolis, INRA, AgroParisTech, Université Paris-Saclay, Paris, France.; Cardiology Department, Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Paris, France.; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.; Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, INSERM, Paris, France.; Integromics Unit, Institute of Cardiometabolism and Nutrition, Paris, France.; Sorbonne Université, IRD, Unité de Modélisation Mathématique et Informatique des Systèmes Complexes, UMMISCO, Paris, France.; Department of Pharmacology, Sorbonne Université, INSERM CIC-1901, UNICO-GRECO Cardio-oncology ProgramAP-HP.Sorbonne, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France.; Department of Cardiology, Rigshopitalet, University of Copenhagen, Copenhagen, Denmark.; Department of Clinical Biochemistry, Rigshopitalet, University of Copenhagen, Copenhagen, Denmark.; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.; Department of Medicine, Bornholms Hospital, Rønne, Denmark.; Nutrition Department, Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Paris, France.; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.; Biobyte Solutions, Heidelberg, Germany.; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.; Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Sahlgrenska Center for Cardiovascular and Metabolic Research, University of Gothenburg, Gothenburg, Sweden.; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden.; Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK.; McGill University and Genome Quebec Innovation Centre, Montréal, Québec, Canada.; Section of Genomic and Environmental Medicine, National Heart & Lung Institute, Faculty of Medicine, Imperial College London, London, UK.; European Genomic Institute for Diabetes, CNRS UMR 8199, INSERM UMR 1283, Institut Pasteur de Lille, Lille University Hospital, University of Lille, Lille, France.; Nutrition and Obesities; Systemic Approaches (NutriOmics), Sorbonne Université, INSERM, Paris, France. [email protected].; Nutrition Department, Assistance Publique Hôpitaux de Paris, Pitie-Salpêtrière Hospital, Paris, France. [email protected].; Medical Department III-Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany. [email protected].; Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München, University of Leipzig, Leipzig, Germany. [email protected].; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. [email protected].; Charité-Universitätsmedizin Berlin, Berlin, Germany. [email protected].; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany. [email protected].; Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea. [email protected].

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