International consensus statement on microbiome testing in clinical practice.

Fergus Shanahan, Antonio Gasbarrini, Luca Masucci, Maurizio Sanguinetti, Eran Segal, Giovanni Cammarota, Gianluca Ianiro, Patrice D Cani, Ilan Youngster, Eran Elinav, Siew C Ng, Francesco Franceschi, Faming Zhang, Liping Zhao, Giovanni Barbara, Georg Zeller, Maria Carmen Collado, Richard Hansen, Jessica Allegretti, Joel Dorè, Robert Knight, Nadeem Kaakoush, Mirjana Rajilic Stojanovic, Aitor Blanco Miguez, Maria Abreu, Simon Mark Baunwall, Josbert Keller, Paul W O'Toole, Hein Tun, Sam P Costello, Jasmohan Bajaj, Maria Vehreschild, Franco Scaldaferri, Jeroen Raes, Francis Megraud, Lorenza Putignani, Edoardo Pasolli, Mireia Valles-Colomer, Francesco Asnicar, Willem M de Vos, Brunella Posteraro, Monika Fischer, Alexander Link, Manimozhiyan Arumugam, Emad El-Omar, Francisco Guarner, Christian Lodberg Hvas, Juozas Kupcinskas, Julian Marchesi, Georgina Hold, Sudarshan Paramsothy, Flavio De Maio, Patrizia Brigidi, Benoit Chassaing, Harry Sokol, Francesca Romana Ponziani, Rinse K Weersma, Tariq Iqbal, Colleen Kelly, Herbert Tilg, Nicola Segata, John Cryan, Peter Malfertheiner, Rupert Leong, Omry Koren, Serena Porcari, Benjamin H Mullish, Sahil Khanna, Dina Kao

Journal: The lancet. Gastroenterology & hepatology 2025;10(2):154-167

PMID: 39647502

Abstract

There is growing interest in the potential exploitation of the gut microbiome as a diagnostic tool in medicine, but evidence supporting its clinical usefulness is scarce. An increasing number of commercial providers offer direct-to-consumer microbiome diagnostic tests without any consensus on their regulation or any proven value in clinical practice, which could result in considerable waste of individual and health-care resources and potential drawbacks in the clinical management of patients. We convened an international multidisciplinary expert panel to standardise best practices of microbiome testing for clinical implementation, including recommendations on general principles and minimum requirements for their provision, indications, pre-testing protocols, method of analyses, reporting of results, and potential clinical value. We also evaluated current knowledge gaps and future directions in this field. We aimed to establish a framework to regulate the provision of microbiome testing and minimise the use of inappropriate tests and pave the way for the evidence-based development and use of human microbiome diagnostics in clinical medicine.

Copyright © 2024 Elsevier Ltd. All rights reserved, including those for text and data mining, AI training, and similar technologies.

Address: Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.; Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK; Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK.; Department CIBIO, University of Trento, Trento, Italy.; Microbiota I-Center (MagIC), Hong Kong Special Administrative Region, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China.; Department of Biochemistry and Microbiology, New Jersey Institute of Food, Nutrition and Health, Rutgers University, New Brunswick, NY, USA.; Division of Molecular and Clinical Medicine, School of Medicine, University of Dundee, Dundee, UK.; APC Microbiome Ireland, Department of Medicine, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland.; Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium; VIB, Center for Microbiology, Leuven, Belgium.; Microbiome Research Centre, University of New South Wales, Sydney, Australia.; Unit of Microbiomics and Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.; Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus Denmark.; Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, Netherlands; Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.; Azrieli Faculty of Medicine Bar-Ilan University, Safed, Israel.; The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China.; Department CIBIO, University of Trento, Trento, Italy; MELIS Department, Pompeu Fabra University, Barcelona, Spain.; Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia, Spain.; Division of Gastroenterology, Indiana University School of Medicine, Indianapolis, IN, USA.; Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA.; Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Microbiome Treatment Centre, University of Birmingham, Edgbaston, UK.; Microbiome-Host Interactions, Institut Pasteur, Université Paris Cité, INSERM, Paris, France.; Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands; Public Health Laboratory, Faculty of Medicine, University of Birmingham, Birmingham, UK.; Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.; Division of Gastroenterology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA.; IRCCS Azienda Ospedaliero, University of Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.; Medical Center for Digestive Diseases, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, China; Key Lab of Holistic Integrative Enterology, Nanjing Medical University, Nanjing, China.; Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; Liver Unit-Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell'Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.; Department of Gastroenterology, The Queen Elizabeth Hospital, Adelaide, South Australia, Australia; Faculty of Health and Medical Sciences, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia.; Department of Gastroenterology and Hepatology, Concord Repatriation General Hospital, Sydney, Australia; Concord Clinical School, University of Sydney, Sydney, Australia.; Edmonton FMT program, Division of Gastroenterology, University of Alberta, Edmonton, AB, Canada.; Gastroenterology Department and Institute for Digestive Research; Lithuanian University of Health Sciences Kaunas, Lithuania.; Division of Pediatrics and the Center for Microbiome Research, Shamir Medical Center, Israel, Faculty of Medical & Health Sciences, Tel-Aviv University, Tel-Aviv, Israel.; Department of Emergency Medicine, Fondazione Policlinico Universitario, Università Cattolica del Sacro Cuore, Rome, Italy.; Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA.; Goethe University Frankfurt, University Hospital Frankfurt, Department II of Internal Medicine, Infectious Diseases, Frankfurt am Main, Germany.; Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University, Magdeburg, Germany.; Department of Laboratory and Infectious Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.; University of Naples Federico II, Department of Agricultural Sciences, Portici, Italy.; Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.; Department of Basic Biotechnological Sciences, Intensive and Perioperative Clinics, Università Cattolica del Sacro Cuore, Rome, Italy.; Department for Biochemical Engineering and Biotechnology, University of Belgrade, Belgrade, Serbia; Faculty of Technology and Metallurgy, University of Belgrade, Belgrade, Serbia.; INSERM U1312 BRIC, Université de Bordeaux, Bordeaux, France.; Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University, Magdeburg, Germany; LMU, University Clinic, Medical Department II, Munich, Germany.; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.; School of Biomedical Sciences, University of New South Wales, Sydney, Australia.; Computer Science and Applied Mathematics Department, Weizmann Institute of Science, Rehovot, Israel.; Division of Gastroenterology, Hepatology, and Nutrition, Virginia Commonwealth University and Richmond VA Medical Center, Richmond, VA, USA.; Department of Gastroenterology, Concord Repatriation General Hospital, Sydney, Australia; MQ Health, Macquarie University Hospital, Sydney, Australia.; APC Microbiome Ireland, Department of Medicine, University College Cork, Cork, Ireland.; Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, Netherlands.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.; Centro Médico Teknon, Barcelona, Spain.; Louvain Drug Research Institute (LDRI), Metabolism and Nutrition Research Group, UCLouvain, Université Catholique de Louvain, Brussels, Belgium; Institute of Experimental and Clinical Research (IREC), UCLouvain, Université Catholique de Louvain, Brussels, Belgium; Walloon Excellence in Life Sciences and BIOtechnology (WELBIO), WELBIO department, WEL Research Institute, Wavre, Belgium.; Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel; Cancer-Microbiome Division, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany.; Laboratory of Microbiology, Wageningen University, Netherlands; Human Microbiome Research Program, University of Helsinki, Finland.; Microbiome Research Centre, St George & Sutherland Clinical Campuses, School of Clinical Medicine, University of New South Wales, Sydney, Australia.; MR Micalis Institut, INRA, Paris-Saclay University, Jouy-En-Josas, France.; Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK.; Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Innsbruck, Austria.; MR Micalis Institut, INRA, Paris-Saclay University, Jouy-En-Josas, France; Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint-Antoine Hospital, Paris, France; Paris Center for Microbiome MedICIsne (PaCeMM) FHU, Paris, France.; Department CIBIO, University of Trento, Trento, Italy; Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy.; Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy. Electronic address: [email protected].

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