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Liu Y, Méric G, Havulinna AS, Teo SM, Åberg F, Ruuskanen M, Sanders J, Zhu Q, Tripathi A, Verspoor K, Cheng S, Jain M, Jousilahti P, Vázquez-Baeza Y, Loomba R, Lahti L, Niiranen T, Salomaa V, Knight R, Inouye M. Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boosting. Cell Metab 2022; 34:719-730.e4. [PMID: 35354069 PMCID: PMC9097589 DOI: 10.1016/j.cmet.2022.03.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/06/2022] [Accepted: 03/08/2022] [Indexed: 02/08/2023]
Abstract
The gut microbiome has shown promise as a predictive biomarker for various diseases. However, the potential of gut microbiota for prospective risk prediction of liver disease has not been assessed. Here, we utilized shallow shotgun metagenomic sequencing of a large population-based cohort (N > 7,000) with ∼15 years of follow-up in combination with machine learning to investigate the predictive capacity of gut microbial predictors individually and in conjunction with conventional risk factors for incident liver disease. Separately, conventional and microbial factors showed comparable predictive capacity. However, microbiome augmentation of conventional risk factors using machine learning significantly improved the performance. Similarly, disease-free survival analysis showed significantly improved stratification using microbiome-augmented models. Investigation of predictive microbial signatures revealed previously unknown taxa for liver disease, as well as those previously associated with hepatic function and disease. This study supports the potential clinical validity of gut metagenomic sequencing to complement conventional risk factors for prediction of liver diseases.
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Affiliation(s)
- Yang Liu
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia.
| | - Guillaume Méric
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia; Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, VIC, Australia; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Aki S Havulinna
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland; Institute of Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Shu Mei Teo
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia; Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Fredrik Åberg
- Transplantation and Liver Surgery Clinic, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Matti Ruuskanen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland; Department of Internal Medicine, University of Turku, Turku, Finland
| | - Jon Sanders
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Anupriya Tripathi
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Karin Verspoor
- School of Computing and Information Systems, University of Melbourne, Melbourne, VIC, Australia; School of Computing Technologies, RMIT University, Melbourne, VIC, Australia
| | - Susan Cheng
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mohit Jain
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Pekka Jousilahti
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA; Department of Computer Science & Engineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Rohit Loomba
- NAFLD Research Center, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Teemu Niiranen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland; Department of Internal Medicine, University of Turku, Turku, Finland; Division of Medicine, Turku University Hospital, Turku, Finland
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA; Department of Computer Science & Engineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia; Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, VIC, Australia; Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Health Data Research UK Cambridge, Wellcome Genome Campus, University of Cambridge, Cambridge, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK; The Alan Turing Institute, London, UK.
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