A multi-omics approach to delineate sputum microbiome-associated asthma inflammatory phenotypes.

Competing Interests: Conflicts of interest: M.I. Abdel-Aziz, S.J.H. Vijverberg, A.H. Neerincx, P. Brinkman, A.H. Wagener, A.R. Sousa, Å.M. Wheelock, AT. Bansal, M. Caruso, J. Corfield, N. Krug, J. Musial, K. Sun, D.E. Shaw, P. Montuschi, R. Lutter, P. Howarth, M. Sanak, I.M. Adcock, P. Chanez and AD. Kraneveld have no conflicts of interest to disclose. J.H. Riley was an employee and a shareholder of GlaxoSmithKline. S. Bates is an employee of Johnson & Johnson and a former employee of GlaxoSmithKline, and holds stock in both companies. S.S. Wagers reports consulting fees from Kings College Hospital NHS Foundation Trust, Academic Medical Research, Aladdin Healthcare Technologies Ltd, AMC Medical Research BV, AMC Medical Research BV P402, Asthma UK, AstraZeneca AB, Athens Medical School, Autobedrijf Verfaillie V-CO BVBA, Boehringer Ingelheim International GmbH, Breathomix BV, Chiesi Farmaceutici S.p.A., CHU de Toulouse, CIRO, Consorcio Centro de Investigación Biomédica en Red, Dawi Iman Automobile, DS Biologicls Ltd, École Polytechnique Fédérale de Lausanne, European Federation of Allergy, European Respiratory Society, European Society for Swallowing Disorders, F. Hoffmann-La Roche AG, FISEVI, Fluidic Analytics Ltd, Foundation for Research and Technology Hellas, Fraunhofer IGB, Fraunhofer ITEM, Fraunhofer-Institut für Produktionstechnologie IPT, GlaxoSmithKline Research & Dev Ltd, Gossamer Bio, Inc, Holland & Knight, Imperial College, Institute for Computer Science and Control, Karolinska Institutet Fakturor, KU Leuven, Longfonds, Maastricht University, MedImmune LLC, Merck Sharp & Dohme Corp., National Heart & Lung Institute, Ninja Hoen, Novartis Pharma AG, OncoRadiomics S.A., Owlstone Medical Limited, PExA AB, Pulmonary Fibrosis Foundation, RISE Research Institutes of Sweden AB, Sanofi US Services Inc., TEVA Branded Pharmaceutical Products R&D Inc., The North West Lung Centre Charity, Three Lakes Foundation Trust, TopMD Precision Medicine Ltd, UCB Biopharma S.P.R.L., UCB Biosciences GmbH, UGent, Umeå University, Univ. Hospital Southampton NHS Foundation Trust, Università Campus Bio-Medico di Roma, Universita Cattolica Del Sacro Cuore, Universität Ulm, Universitätsklinikum Würzburg, University College London, University Hospital Southampton, University of Bern, University of Edinburgh, University of Hull, University of Leicester, University of Loughborough, University of Luxembourg, University of Manchester, University of Nottingham, VITO NV, Vlaams Brabant, Dienst Europa, Kings College Hospital NHS Foundation Trust, and Academic Medical Research paid to his company (BioSci Consulting); outside the submitted work. B. De Meulder and C. Auffray have received grants from Innovative Medicines Initiative (IMI U-BIOPRED grant number 115010 and IMI eTRIKS grant number 115446), during the conduct of the study. M. Uddin is an employee of AstraZeneca and holds shares in the company. I. Horvath has received personal honoraria for lectures from AstraZeneca, Chiesi, GSK, Novartis and MSD, and had unpaid leadership or fiduciary roles in European Respiratory Society, Hungarian Respiratory Society, and Hungarian Association of Medical Societies. T. Sandström has received fees from lecturing for Boehringer Ingelheim with payments to clinic/institution. S.J. Fowler has received honoraria for lectures from AstraZeneca, Novartis, Teva, Boehringer Ingelheim and Chiesi, and has received support to attend ERS and BTS meetings from AstraZeneca and Chiesi, and participated in the advisory board of Chiesi. R. Djukanovic is a co-founder of and has stocks with Synairgen, a University of Southampton spin out company, which is funding a phase 3 trial of nebulised interferon beta for treatment of hospitalised COVID-19 patients and a community based study of PCR positive individuals to see if treatment can improve clinical outcomes, and is a member (without receiving funding) of the Urgent Public Health (UPH) panel that approves studies under a priority badge, and has received fees for consultancy services from TEVA Pharmaceuticals, Sanofi, Boehringer and Novartis, and has received grants (paid to his institution) from IMI funded EU project, UBIOPRED, MRC funded project on COPD: COPD-MAP and Novartis to Study of mechanisms of action of Omalizumab, and has received fees for lectures on mechanisms of action of Xolair for Novartis and a lecture in symposium on mechanisms of asthma for Teva. P. Skipp is a shareholder in TopMD Precision Medicine. K.F. Chung reports funding during the conduct of the study paid to his institution from the Innovative Medicines Initiative (IMI) Joint Undertaking under grant agreement number 115010. P.J. Sterk reports funding during the conduct of the study paid to his institution from Innovative Medicines Initiative (IMI), which is public-private funding provided by the EU and the European Federation of Pharmaceutical Industries and Associations (EFPIA), and is a scientific adviser and has an officially non-substantial interest in the start-up company Breathomix BV, The Netherlands; outside the submitted work. A.H. Maitland-van der Zee has received grants from Health Holland and she is the PI of a P4O2 (Precision Medicine for more Oxygen) public private partnership sponsored by Health Holland involving many private partners that contribute in cash and/or in kind (Boehringer Ingelheim, Breathomix, Fluidda, Ortec Logiqcare, Philips, Quantib-U, Smartfish, SODAQ, Thirona, TopMD and Novartis), received unrestricted research grants from GSK, Boehringer Ingelheim and Vertex, received consulting fees paid to her institution from Boehringer Ingelheim and AstraZeneca, and received honoraria for lectures paid to her institution from GlaxoSmithKline; outside the submitted work.