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Karjalainen MK, Karthikeyan S, Oliver-Williams C, Sliz E, Allara E, Fung WT, Surendran P, Zhang W, Jousilahti P, Kristiansson K, Salomaa V, Goodwin M, Hughes DA, Boehnke M, Fernandes Silva L, Yin X, Mahajan A, Neville MJ, van Zuydam NR, de Mutsert R, Li-Gao R, Mook-Kanamori DO, Demirkan A, Liu J, Noordam R, Trompet S, Chen Z, Kartsonaki C, Li L, Lin K, Hagenbeek FA, Hottenga JJ, Pool R, Ikram MA, van Meurs J, Haller T, Milaneschi Y, Kähönen M, Mishra PP, Joshi PK, Macdonald-Dunlop E, Mangino M, Zierer J, Acar IE, Hoyng CB, Lechanteur YTE, Franke L, Kurilshikov A, Zhernakova A, Beekman M, van den Akker EB, Kolcic I, Polasek O, Rudan I, Gieger C, Waldenberger M, Asselbergs FW, Hayward C, Fu J, den Hollander AI, Menni C, Spector TD, Wilson JF, Lehtimäki T, Raitakari OT, Penninx BWJH, Esko T, Walters RG, Jukema JW, Sattar N, Ghanbari M, Willems van Dijk K, Karpe F, McCarthy MI, Laakso M, Järvelin MR, Timpson NJ, Perola M, Kooner JS, Chambers JC, van Duijn C, Slagboom PE, Boomsma DI, Danesh J, Ala-Korpela M, Butterworth AS, Kettunen J. Genome-wide characterization of circulating metabolic biomarkers. Nature 2024; 628:130-138. [PMID: 38448586 PMCID: PMC10990933 DOI: 10.1038/s41586-024-07148-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/01/2024] [Indexed: 03/08/2024]
Abstract
Genome-wide association analyses using high-throughput metabolomics platforms have led to novel insights into the biology of human metabolism1-7. This detailed knowledge of the genetic determinants of systemic metabolism has been pivotal for uncovering how genetic pathways influence biological mechanisms and complex diseases8-11. Here we present a genome-wide association study for 233 circulating metabolic traits quantified by nuclear magnetic resonance spectroscopy in up to 136,016 participants from 33 cohorts. We identify more than 400 independent loci and assign probable causal genes at two-thirds of these using manual curation of plausible biological candidates. We highlight the importance of sample and participant characteristics that can have significant effects on genetic associations. We use detailed metabolic profiling of lipoprotein- and lipid-associated variants to better characterize how known lipid loci and novel loci affect lipoprotein metabolism at a granular level. We demonstrate the translational utility of comprehensively phenotyped molecular data, characterizing the metabolic associations of intrahepatic cholestasis of pregnancy. Finally, we observe substantial genetic pleiotropy for multiple metabolic pathways and illustrate the importance of careful instrument selection in Mendelian randomization analysis, revealing a putative causal relationship between acetone and hypertension. Our publicly available results provide a foundational resource for the community to examine the role of metabolism across diverse diseases.
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Affiliation(s)
- Minna K Karjalainen
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland.
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland.
- Northern Finland Birth Cohorts, Arctic Biobank, Infrastructure for Population Studies, Faculty of Medicine, University of Oulu, Oulu, Finland.
| | - Savita Karthikeyan
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Clare Oliver-Williams
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Public Health Specialty Training Programme, Cambridge, UK
| | - Eeva Sliz
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Elias Allara
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Wing Tung Fung
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, UK
| | - Pekka Jousilahti
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Kati Kristiansson
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Matt Goodwin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - David A Hughes
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Lilian Fernandes Silva
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Xianyong Yin
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Jiangsu, China
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Matt J Neville
- NIHR Oxford Biomedical Research Centre, OUHFT Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Natalie R van Zuydam
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Ayse Demirkan
- Surrey Institute for People-Centred AI, University of Surrey, Guildford, UK
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, University of Surrey, Guildford, UK
| | - Jun Liu
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Stella Trompet
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Christiana Kartsonaki
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Peking University Center for Public Health and Epidemic Preparedness and Response, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Peking University, Ministry of Education, Beijing, China
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Toomas Haller
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mika Kähönen
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Pashupati P Mishra
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Peter K Joshi
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Erin Macdonald-Dunlop
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, UK
| | - Jonas Zierer
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Ilhan E Acar
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yara T E Lechanteur
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marian Beekman
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Erik B van den Akker
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
- Center for Computational Biology, Leiden University Medical Center, Leiden, The Netherlands
- The Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Ivana Kolcic
- Department of Public Health, School of Medicine, University of Split, Split, Croatia
| | - Ozren Polasek
- Department of Public Health, School of Medicine, University of Split, Split, Croatia
| | - Igor Rudan
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Folkert W Asselbergs
- Amsterdam University Medical Centers, Department of Cardiology, University of Amsterdam, Amsterdam, The Netherlands
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jingyuan Fu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
- Genomics Research Center, Abbvie, Cambridge, MA, USA
| | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - James F Wilson
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, Scotland
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Terho Lehtimäki
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Olli T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- InFLAMES Research Flagship, University of Turku, Turku, Finland
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Tonu Esko
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Heart Institute, Utrecht, The Netherlands
| | - Naveed Sattar
- School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Internal Medicine, Division Endocrinology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Fredrik Karpe
- NIHR Oxford Biomedical Research Centre, OUHFT Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | - Marjo-Riitta Järvelin
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
- Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Markus Perola
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Diabetes and Obesity Research Program, University of Helsinki, Helsinki, Finland
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - John C Chambers
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, London, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Cornelia van Duijn
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - P Eline Slagboom
- Section of Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
- Amsterdam Reproduction and Development (AR&D) Research Institute, Amsterdam, The Netherlands
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Mika Ala-Korpela
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Johannes Kettunen
- Systems Epidemiology, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
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2
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Warmbrunn MV, Boulund U, Aron-Wisnewsky J, de Goffau MC, Abeka RE, Davids M, Bresser LRF, Levin E, Clement K, Galenkamp H, Ferwerda B, van den Born BJJH, Kurilshikov A, Fu J, Zwinderman AH, Soeters MR, van Raalte DH, Herrema H, Groen AK, Nieuwdorp M. Networks of gut bacteria relate to cardiovascular disease in a multi-ethnic population: the HELIUS study. Cardiovasc Res 2024; 120:372-384. [PMID: 38289866 PMCID: PMC10981523 DOI: 10.1093/cvr/cvae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/25/2023] [Accepted: 11/30/2023] [Indexed: 02/01/2024] Open
Abstract
AIMS Gut microbiota have been linked to blood lipid levels and cardiovascular diseases (CVDs). The composition and abundance of gut microbiota trophic networks differ between ethnicities. We aim to evaluate the relationship between gut microbiotal trophic networks and CVD phenotypes. METHODS AND RESULTS We included cross-sectional data from 3860 individuals without CVD history from 6 ethnicities living in the Amsterdam region participating in the prospective Healthy Life in Urban Setting (HELIUS) study. Genetic variants were genotyped, faecal gut microbiota were profiled, and blood and anthropometric parameters were measured. A machine learning approach was used to assess the relationship between CVD risk (Framingham score) and gut microbiota stratified by ethnicity. Potential causal relationships between gut microbiota composition and CVD were inferred by performing two-sample Mendelian randomization with hard CVD events from the Pan-UK Biobank and microbiome genome-wide association studies summary data from a subset of the HELIUS cohort (n = 4117). Microbial taxa identified to be associated with CVD by machine learning and Mendelian randomization were often ethnic-specific, but some concordance across ethnicities was found. The microbes Akkermansia muciniphila and Ruminococcaceae UCG-002 were protective against ischaemic heart disease in African-Surinamese and Moroccans, respectively. We identified a strong inverse association between blood lipids, CVD risk, and the combined abundance of the correlated microbes Christensenellaceae-Methanobrevibacter-Ruminococcaceae (CMR). The CMR cluster was also identified in two independent cohorts and the association with triglycerides was replicated. CONCLUSION Certain gut microbes can have a potentially causal relationship with CVD events, with possible ethnic-specific effects. We identified a trophic network centred around Christensenellaceae, Methanobrevibacter, and various Ruminococcaceae, frequently lacking in South-Asian Surinamese, to be protective against CVD risk and associated with low triglyceride levels.
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Affiliation(s)
- Moritz V Warmbrunn
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ulrika Boulund
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism (AGEM) Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Judith Aron-Wisnewsky
- Nutrition and Obesities: Systemic Approaches Research Unit (Nutriomics), Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Paris, France
- Nutrition Department, Assistantea Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Centres de Recherche en Nutrition Humaine, Paris, Ile de France, France
| | - Marcus C de Goffau
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- HorAIzon BV, 2625 GZ Delft, The Netherlands
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Meibergdreef 69, 1105 BK Amsterdam, The Netherlands
| | - Rosamel E Abeka
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Mark Davids
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Lucas R F Bresser
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- HorAIzon BV, 2625 GZ Delft, The Netherlands
| | - Evgeni Levin
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- HorAIzon BV, 2625 GZ Delft, The Netherlands
| | - Karine Clement
- Nutrition and Obesities: Systemic Approaches Research Unit (Nutriomics), Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Paris, France
- Nutrition Department, Assistantea Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Centres de Recherche en Nutrition Humaine, Paris, Ile de France, France
| | - Henrike Galenkamp
- Department of Public Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Bart Ferwerda
- Department of Clinical Epidemiology and Biostatistics, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Bert-Jan J H van den Born
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Alexander Kurilshikov
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Aeilko H Zwinderman
- Department of Public Health, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Maarten R Soeters
- Department of Endocrinology and Metabolism, Internal Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Daniel H van Raalte
- Department of Internal Medicine, Amsterdam University Medical Center (UMC), Vrije Universiteit (VU) University Medical Center, Amsterdam, The Netherlands
| | - Hilde Herrema
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Albert K Groen
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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3
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Garmaeva S, Sinha T, Gulyaeva A, Kuzub N, Spreckels JE, Andreu-Sánchez S, Gacesa R, Vich Vila A, Brushett S, Kruk M, Dekens J, Sikkema J, Kuipers F, Shkoporov AN, Hill C, Scherjon S, Wijmenga C, Fu J, Kurilshikov A, Zhernakova A. Transmission and dynamics of mother-infant gut viruses during pregnancy and early life. Nat Commun 2024; 15:1945. [PMID: 38431663 PMCID: PMC10908809 DOI: 10.1038/s41467-024-45257-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/16/2024] [Indexed: 03/05/2024] Open
Abstract
Early development of the gut ecosystem is crucial for lifelong health. While infant gut bacterial communities have been studied extensively, the infant gut virome remains under-explored. To study the development of the infant gut virome over time and the factors that shape it, we longitudinally assess the composition of gut viruses and their bacterial hosts in 30 women during and after pregnancy and in their 32 infants during their first year of life. Using shotgun metagenomic sequencing applied to dsDNA extracted from Virus-Like Particles (VLPs) and bacteria, we generate 205 VLP metaviromes and 322 total metagenomes. With this data, we show that while the maternal gut virome composition remains stable during late pregnancy and after birth, the infant gut virome is dynamic in the first year of life. Notably, infant gut viromes contain a higher abundance of active temperate phages compared to maternal gut viromes, which decreases over the first year of life. Moreover, we show that the feeding mode and place of delivery influence the gut virome composition of infants. Lastly, we provide evidence of co-transmission of viral and bacterial strains from mothers to infants, demonstrating that infants acquire some of their virome from their mother's gut.
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Affiliation(s)
- Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Anastasia Gulyaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Nataliia Kuzub
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Johanne E Spreckels
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Siobhan Brushett
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Health Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marloes Kruk
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jackie Dekens
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- University Medical Center Groningen, Center for Development and Innovation, Groningen, Netherlands
| | - Jan Sikkema
- University Medical Center Groningen, Center for Development and Innovation, Groningen, Netherlands
| | - Folkert Kuipers
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Andrey N Shkoporov
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Sicco Scherjon
- Department of Obstetrics and Gynecology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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4
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Fernández-Pato A, Sinha T, Gacesa R, Andreu-Sánchez S, Gois MFB, Gelderloos-Arends J, Jansen DBH, Kruk M, Jaeger M, Joosten LAB, Netea MG, Weersma RK, Wijmenga C, Harmsen HJM, Fu J, Zhernakova A, Kurilshikov A. Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses. Sci Rep 2024; 14:3911. [PMID: 38366085 PMCID: PMC10873414 DOI: 10.1038/s41598-024-54353-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/12/2024] [Indexed: 02/18/2024] Open
Abstract
The lack of standardization in the methods of DNA extraction from fecal samples represents the major source of experimental variation in the microbiome research field. In this study, we aimed to compare the metagenomic profiles and microbiome-phenotype associations obtained by applying two commercially available DNA extraction kits: the AllPrep DNA/RNA Mini Kit (APK) and the QIAamp Fast DNA Stool Mini Kit (FSK). Using metagenomic sequencing data available from 745 paired fecal samples from two independent population cohorts, Lifelines-DEEP (LLD, n = 292) and the 500 Functional Genomics project (500FG, n = 453), we confirmed significant differences in DNA yield and the recovered microbial communities between protocols, with the APK method resulting in a higher DNA concentration and microbial diversity. Further, we observed a massive difference in bacterial relative abundances at species-level between the APK and the FSK protocols, with > 75% of species differentially abundant between protocols in both cohorts. Specifically, comparison with a standard mock community revealed that the APK method provided higher accuracy in the recovery of microbial relative abundances, with the absence of a bead-beating step in the FSK protocol causing an underrepresentation of gram-positive bacteria. This heterogeneity in the recovered microbial composition led to remarkable differences in the association with anthropometric and lifestyle phenotypes. The results of this study further reinforce that the choice of DNA extraction method impacts the metagenomic profile of human gut microbiota and highlight the importance of harmonizing protocols in microbiome studies.
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Affiliation(s)
- Asier Fernández-Pato
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Milla F Brandao Gois
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Jody Gelderloos-Arends
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Dianne B H Jansen
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Marloes Kruk
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Martin Jaeger
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Hermie J M Harmsen
- Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9713GZ, the Netherlands.
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5
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Brushett S, Gacesa R, Vich Vila A, Brandao Gois M, Andreu-Sánchez S, Swarte J, Klaassen M, Collij V, Sinha T, Bolte L, Wu J, Swertz M, de Kroon M, Reijneveld S, Wijmenga C, Weersma R, Fu J, van Loo H, Kurilshikov A, Zhernakova A. Gut feelings: the relations between depression, anxiety, psychotropic drugs and the gut microbiome. Gut Microbes 2023; 15:2281360. [PMID: 38017662 PMCID: PMC10730195 DOI: 10.1080/19490976.2023.2281360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023] Open
Abstract
The gut microbiome is involved in the bi-directional relationship of the gut - brain axis. As most studies of this relationship are small and do not account for use of psychotropic drugs (PTDs), we explored the relations of the gut microbiome with several internalizing disorders, while adjusting for PTDs and other relevant medications, in 7,656 Lifelines participants from the Northern Netherlands (5,522 controls and 491 participants with at least one internalizing disorder). Disorders included dysthymia, major depressive disorder (MDD), any depressive disorder (AnyDep: dysthymia or MDD), generalized anxiety disorder (GAD) and any anxiety disorder (AnyAnx: GAD, social phobia and panic disorder). Compared to controls, 17 species were associated with depressive disorders and 3 were associated with anxiety disorders. Around 90% of these associations remained significant (FDR <0.05) after adjustment for PTD use, suggesting that the disorders, not PTD use, drove these associations. Negative associations were observed for the butyrate-producing bacteria Ruminococcus bromii in participants with AnyDep and for Bifidobacterium bifidum in AnyAnx participants, along with many others. Tryptophan and glutamate synthesis modules and the 3,4-Dihydroxyphenylacetic acid synthesis module (related to dopamine metabolism) were negatively associated with MDD and/or dysthymia. After additional adjustment for functional gastrointestinal disorders and irritable bowel syndrome, these relations remained either statistically (FDR <0.05) or nominally (P < 0.05) significant. Overall, multiple bacterial species and functional modules were associated with internalizing disorders, including gut - brain relevant components, while associations to PTD use were moderate. These findings suggest that internalizing disorders rather than PTDs are associated with gut microbiome differences relative to controls.
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Affiliation(s)
- S. Brushett
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Health Sciences, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - R. Gacesa
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - A. Vich Vila
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - M.F. Brandao Gois
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - S. Andreu-Sánchez
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - J.C. Swarte
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - M.A.Y. Klaassen
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - V. Collij
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - T. Sinha
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - L.A. Bolte
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - J. Wu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - M. Swertz
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M.L.A. de Kroon
- Department of Health Sciences, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - S.A. Reijneveld
- Department of Health Sciences, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - C. Wijmenga
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - R.K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - J. Fu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - H.M. van Loo
- Department of Psychiatry, Interdisciplinary Center Psychopathology and Emotion regulation, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - A. Kurilshikov
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - A. Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
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6
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Spreckels JE, Fernández-Pato A, Kruk M, Kurilshikov A, Garmaeva S, Sinha T, Ghosh H, Harmsen H, Fu J, Gacesa R, Zhernakova A. Analysis of microbial composition and sharing in low-biomass human milk samples: a comparison of DNA isolation and sequencing techniques. ISME Commun 2023; 3:116. [PMID: 37945978 PMCID: PMC10636111 DOI: 10.1038/s43705-023-00325-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Human milk microbiome studies are currently hindered by low milk bacterial/human cell ratios and often rely on 16S rRNA gene sequencing, which limits downstream analyses. Here, we aimed to find a method to study milk bacteria and assess bacterial sharing between maternal and infant microbiota. We tested four DNA isolation methods, two bacterial enrichment methods and three sequencing methods on mock communities, milk samples and negative controls. Of the four DNA isolation kits, the DNeasy PowerSoil Pro (PS) and MagMAX Total Nucleic Acid Isolation (MX) kits provided consistent 16S rRNA gene sequencing results with low contamination. Neither enrichment method substantially decreased the human metagenomic sequencing read-depth. Long-read 16S-ITS-23S rRNA gene sequencing biased the mock community composition but provided consistent results for milk samples, with little contamination. In contrast to 16S rRNA gene sequencing, 16S-ITS-23S rRNA gene sequencing of milk, infant oral, infant faecal and maternal faecal DNA from 14 mother-infant pairs provided sufficient resolution to detect significantly more frequent sharing of bacteria between related pairs compared to unrelated pairs. In conclusion, PS or MX kit-DNA isolation followed by 16S rRNA gene sequencing reliably characterises human milk microbiota, and 16S-ITS-23S rRNA gene sequencing enables studies of bacterial transmission in low-biomass samples.
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Grants
- This study was supported by funds from the Dutch Research Council (NWO-VIDI grant 016.178.056 to A.Z., NWO-VICI grant VI.C.202.022 to J.F., NWO gravitation grant Exposome-NL 024.004.017 to A.K. and A.Z., NWO gravitation grant Netherlands Organ-on-Chip Initiative 024.003.001 to J.F.), the Dutch Heart Foundation (IN-CONTROL CVON2018-27 to J.F.), the European Research Council (ERC starting grant 715772 to A.Z., ERC consolidator grant 101001678 to J.F.), an EASI-Genomics grant (PID7780 to T.S. and A.Z.), the De-Cock Hadders foundation (2021-57 to J.E.S., 2021-08 to S.G.), the International Society for Research in Human Milk and Lactation (ISRHML, personal grant to J.E.S), the Winston Bakker Fonds (WB-08, granted to T.S.), and the European Union’s Horizon 2020 research innovation program (824110). S.G. and T.S. hold scholarships from the Graduate School of Medical Sciences and the Junior Scientific Masterclass of the University of Groningen, the Netherlands, respectively. The Lifelines NEXT cohort study received funds from the University Medical Center Groningen Hereditary Metabolic Diseases Fund, Health~Holland (Top Sector Life Sciences and Health), the Ubbo Emmius Foundation, the European Union, the Northern Netherlands Alliance (SNN), the provinces of Friesland and Groningen, the municipality of Groningen, Philips, and the Société des Produits Nestlé.
- De-Cock Hadders foundation (2021-57) International Society of Research in Human Milk and Lactation (ISRHML personal grant)
- Dutch Research Council (NWO gravitation grant Exposome-NL 024.004.017)
- De-Cock Hadders foundation (2021-08) University of Groningen Graduate School of Medical Sciences (scholarship)
- EASI-Genomics (grant PID7780) Winston Bakker Fonds (WB-08) University of Groningen Junior Scientific Masterclass (scholarship)
- Dutch Research Council (NWO-VICI grant VI.C.202.022) Dutch Research Council (NWO gravitation grant Netherlands Organ-on-Chip Initiative 024.003.001) European Research Council (ERC consolidator grant 101001678)
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Affiliation(s)
- Johanne E Spreckels
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Asier Fernández-Pato
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Marloes Kruk
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Sanzhima Garmaeva
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Hiren Ghosh
- Medical Center - University of Freiburg, Institute for Infection Prevention and Hospital Epidemiology, Freiburg, Germany
| | - Hermie Harmsen
- Department of Medical Microbiology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands.
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7
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Gois MFB, Fernández-Pato A, Huss A, Gacesa R, Wijmenga C, Weersma RK, Fu J, Vermeulen RCH, Zhernakova A, Lenters VC, Kurilshikov A. Impact of occupational pesticide exposure on the human gut microbiome. Front Microbiol 2023; 14:1223120. [PMID: 37637104 PMCID: PMC10448898 DOI: 10.3389/fmicb.2023.1223120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
The rising use of pesticides in modern agriculture has led to a shift in disease burden in which exposure to these chemicals plays an increasingly important role. The human gut microbiome, which is partially responsible for the biotransformation of xenobiotics, is also known to promote biotransformation of environmental pollutants. Understanding the effects of occupational pesticide exposure on the gut microbiome can thus provide valuable insights into the mechanisms underlying the impact of pesticide exposure on health. Here we investigate the impact of occupational pesticide exposure on human gut microbiome composition in 7198 participants from the Dutch Microbiome Project of the Lifelines Study. We used job-exposure matrices in combination with occupational codes to retrieve categorical and cumulative estimates of occupational exposures to general pesticides, herbicides, insecticides and fungicides. Approximately 4% of our cohort was occupationally exposed to at least one class of pesticides, with predominant exposure to multiple pesticide classes. Most participants reported long-term employment, suggesting a cumulative profile of exposure. We demonstrate that contact with insecticides, fungicides and a general "all pesticides" class was consistently associated with changes in the gut microbiome, showing significant associations with decreased alpha diversity and a differing beta diversity. We also report changes in the abundance of 39 different bacterial taxa upon exposure to the different pesticide classes included in this study. Together, the extent of statistically relevant associations between gut microbial changes and pesticide exposure in our findings highlights the impact of these compounds on the human gut microbiome.
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Affiliation(s)
- Milla F. Brandao Gois
- Department of Genetics and Department of Gastroenterology and Hepatology University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Asier Fernández-Pato
- Department of Genetics and Department of Gastroenterology and Hepatology University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Anke Huss
- Department of Population Health Sciences, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, Netherlands
| | - Ranko Gacesa
- Department of Genetics and Department of Gastroenterology and Hepatology University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Cisca Wijmenga
- Department of Genetics and Department of Gastroenterology and Hepatology University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Rinse K. Weersma
- Department of Genetics and Department of Gastroenterology and Hepatology University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Jingyuan Fu
- Department of Genetics and Department of Gastroenterology and Hepatology University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Roel C. H. Vermeulen
- Department of Population Health Sciences, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, Netherlands
| | - Alexandra Zhernakova
- Department of Genetics and Department of Gastroenterology and Hepatology University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Virissa C. Lenters
- Department of Population Health Sciences, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, Netherlands
| | - Alexander Kurilshikov
- Department of Genetics and Department of Gastroenterology and Hepatology University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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8
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Andreu-Sánchez S, Bourgonje AR, Vogl T, Kurilshikov A, Leviatan S, Ruiz-Moreno AJ, Hu S, Sinha T, Vich Vila A, Klompus S, Kalka IN, de Leeuw K, Arends S, Jonkers I, Withoff S, Brouwer E, Weinberger A, Wijmenga C, Segal E, Weersma RK, Fu J, Zhernakova A. Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire. Immunity 2023; 56:1376-1392.e8. [PMID: 37164013 DOI: 10.1016/j.immuni.2023.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/13/2022] [Accepted: 04/06/2023] [Indexed: 05/12/2023]
Abstract
Phage-displayed immunoprecipitation sequencing (PhIP-seq) has enabled high-throughput profiling of human antibody repertoires. However, a comprehensive overview of environmental and genetic determinants shaping human adaptive immunity is lacking. In this study, we investigated the effects of genetic, environmental, and intrinsic factors on the variation in human antibody repertoires. We characterized serological antibody repertoires against 344,000 peptides using PhIP-seq libraries from a wide range of microbial and environmental antigens in 1,443 participants from a population cohort. We detected individual-specificity, temporal consistency, and co-housing similarities in antibody repertoires. Genetic analyses showed the involvement of the HLA, IGHV, and FUT2 gene regions in antibody-bound peptide reactivity. Furthermore, we uncovered associations between phenotypic factors (including age, cell counts, sex, smoking behavior, and allergies, among others) and particular antibody-bound peptides. Our results indicate that human antibody epitope repertoires are shaped by both genetics and environmental exposures and highlight specific signatures of distinct phenotypes and genotypes.
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Affiliation(s)
- Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria; Center for Cancer Research, Medical University of Vienna, Wien, Austria.
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Angel J Ruiz-Moreno
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shixian Hu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shelley Klompus
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris N Kalka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Karina de Leeuw
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Suzanne Arends
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Iris Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Elisabeth Brouwer
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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9
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Bourgonje AR, Andreu-Sánchez S, Vogl T, Hu S, Vich Vila A, Gacesa R, Leviatan S, Kurilshikov A, Klompus S, Kalka IN, van Dullemen HM, Weinberger A, Visschedijk MC, Festen EAM, Faber KN, Wijmenga C, Dijkstra G, Segal E, Fu J, Zhernakova A, Weersma RK. Phage-display immunoprecipitation sequencing of the antibody epitope repertoire in inflammatory bowel disease reveals distinct antibody signatures. Immunity 2023; 56:1393-1409.e6. [PMID: 37164015 DOI: 10.1016/j.immuni.2023.04.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/13/2022] [Accepted: 04/14/2023] [Indexed: 05/12/2023]
Abstract
Inflammatory bowel diseases (IBDs), e.g., Crohn's disease (CD) and ulcerative colitis (UC), are chronic immune-mediated inflammatory diseases. A comprehensive overview of an IBD-specific antibody epitope repertoire is, however, lacking. Using high-throughput phage-display immunoprecipitation sequencing (PhIP-Seq), we identified antibodies against 344,000 antimicrobial, immune, and food antigens in 497 individuals with IBD compared with 1,326 controls. IBD was characterized by 373 differentially abundant antibody responses (202 overrepresented and 171 underrepresented), with 17% shared by both IBDs, 55% unique to CD, and 28% unique to UC. Antibody reactivities against bacterial flagellins dominated in CD and were associated with ileal involvement, fibrostenotic disease, and anti-Saccharomyces cerevisiae antibody positivity, but not with fecal microbiome composition. Antibody epitope repertoires accurately discriminated CD from controls (area under the curve [AUC] = 0.89), and similar discrimination was achieved when using only ten antibodies (AUC = 0.87). Individuals with IBD thus show a distinct antibody repertoire against selected peptides, allowing clinical stratification and discovery of immunological targets.
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Affiliation(s)
- Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria; Center for Cancer Research, Medical University of Vienna, Wien, Austria
| | - Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shelley Klompus
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris N Kalka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hendrik M van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Marijn C Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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10
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Doestzada M, Zhernakova DV, C L van den Munckhof I, Wang D, Kurilshikov A, Chen L, Bloks VW, van Faassen M, Rutten JHW, Joosten LAB, Netea MG, Wijmenga C, Riksen NP, Zhernakova A, Kuipers F, Fu J. Systematic analysis of relationships between plasma branched-chain amino acid concentrations and cardiometabolic parameters: an association and Mendelian randomization study. BMC Med 2022; 20:485. [PMID: 36522747 PMCID: PMC9753387 DOI: 10.1186/s12916-022-02688-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Branched-chain amino acids (BCAAs; valine, leucine, and isoleucine) are essential amino acids that are associated with an increased risk of cardiometabolic diseases (CMD). However, there are still only limited insights into potential direct associations between BCAAs and a wide range of CMD parameters, especially those remaining after correcting for covariates and underlying causal relationships. METHODS To shed light on these relationships, we systematically characterized the associations between plasma BCAA concentrations and a large panel of 537 CMD parameters (including atherosclerosis-related parameters, fat distribution, plasma cytokine concentrations and cell counts, circulating concentrations of cardiovascular-related proteins and plasma metabolites) in 1400 individuals from the Dutch population cohort LifeLines DEEP and 294 overweight individuals from the 300OB cohort. After correcting for age, sex, and BMI, we assessed associations between individual BCAAs and CMD parameters. We further assessed the underlying causality using Mendelian randomization. RESULTS A total of 838 significant associations were detected for 409 CMD parameters. BCAAs showed both common and specific associations, with the most specific associations being detected for isoleucine. Further, we found that obesity status substantially affected the strength and direction of associations for valine, which cannot be corrected for using BMI as a covariate. Subsequent univariable Mendelian randomization (UVMR), after removing BMI-associated SNPs, identified seven significant causal relationships from four CMD traits to BCAA levels, mostly for diabetes-related parameters. However, no causal effects of BCAAs on CMD parameters were supported. CONCLUSIONS Our cross-sectional association study reports a large number of associations between BCAAs and CMD parameters. Our results highlight some specific associations for isoleucine, as well as obesity-specific effects for valine. MR-based causality analysis suggests that altered BCAA levels can be a consequence of diabetes and alteration in lipid metabolism. We found no MR evidence to support a causal role for BCAAs in CMD. These findings provide evidence to (re)evaluate the clinical importance of individual BCAAs in CMD diagnosis, prevention, and treatment.
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Affiliation(s)
- Marwah Doestzada
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.,Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Daria V Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.,Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO University, St. Petersburg, Russia
| | - Inge C L van den Munckhof
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Daoming Wang
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.,Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Lianmin Chen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.,Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Vincent W Bloks
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Martijn van Faassen
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Joost H W Rutten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands.,Department for Genomics Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany.,Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Craiova, Romania
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Niels P Riksen
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Folkert Kuipers
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, European Institute of Healthy Ageing (ERIBA), Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands. .,Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
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11
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Swarte JC, Li Y, Hu S, Björk JR, Gacesa R, Vich Vila A, Douwes RM, Collij V, Kurilshikov A, Post A, Klaassen MAY, Eisenga MF, Gomes-Neto AW, Kremer D, Jansen BH, Knobbe TJ, Berger SP, Sanders JSF, Heiner-Fokkema MR, Porte RJ, Cuperus FJC, de Meijer VE, Wijmenga C, Festen EAM, Zhernakova A, Fu J, Harmsen HJM, Blokzijl H, Bakker SJL, Weersma RK. Gut microbiome dysbiosis is associated with increased mortality after solid organ transplantation. Sci Transl Med 2022; 14:eabn7566. [PMID: 36044594 DOI: 10.1126/scitranslmed.abn7566] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Organ transplantation is a life-saving treatment for patients with end-stage disease, but survival rates after transplantation vary considerably. There is now increasing evidence that the gut microbiome is linked to the survival of patients undergoing hematopoietic cell transplant, yet little is known about the role of the gut microbiome in solid organ transplantation. We analyzed 1370 fecal samples from 415 liver and 672 renal transplant recipients using shotgun metagenomic sequencing to assess microbial taxonomy, metabolic pathways, antibiotic resistance genes, and virulence factors. To quantify taxonomic and metabolic dysbiosis, we also analyzed 1183 age-, sex-, and body mass index-matched controls from the same population. In addition, a subset of 78 renal transplant recipients was followed longitudinally from pretransplantation to 24 months after transplantation. Our data showed that both liver and kidney transplant recipients suffered from gut dysbiosis, including lower microbial diversity, increased abundance of unhealthy microbial species, decreased abundance of important metabolic pathways, and increased prevalence and diversity of antibiotic resistance genes and virulence factors. These changes were found to persist up to 20 years after transplantation. Last, we demonstrated that the use of immunosuppressive drugs was associated with the observed dysbiosis and that the extent of dysbiosis was associated with increased mortality after transplantation. This study represents a step toward potential microbiome-targeted interventions that might influence the outcomes of recipients of solid organ transplantation.
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Affiliation(s)
- J Casper Swarte
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Yanni Li
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Rianne M Douwes
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Valerie Collij
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Adrian Post
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Marjolein A Y Klaassen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Michele F Eisenga
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - António W Gomes-Neto
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Daan Kremer
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Bernadien H Jansen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Tim J Knobbe
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Stefan P Berger
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Jan-Stephan F Sanders
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - M Rebecca Heiner-Fokkema
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Robert J Porte
- Department of Surgery, Section of Hepatobiliary Surgery and Liver Transplantation, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Frans J C Cuperus
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Vincent E de Meijer
- Department of Surgery, Section of Hepatobiliary Surgery and Liver Transplantation, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Cisca Wijmenga
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Hans Blokzijl
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Stephan J L Bakker
- Division of Nephrology, Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
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12
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Lopera-Maya EA, Kurilshikov A, van der Graaf A, Hu S, Andreu-Sánchez S, Chen L, Vila AV, Gacesa R, Sinha T, Collij V, Klaassen MAY, Bolte LA, Gois MFB, Neerincx PBT, Swertz MA, Harmsen HJM, Wijmenga C, Fu J, Weersma RK, Zhernakova A, Sanna S. Author Correction: Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project. Nat Genet 2022; 54:1448. [PMID: 35879415 DOI: 10.1038/s41588-022-01164-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Esteban A Lopera-Maya
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adriaan van der Graaf
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shixian Hu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lianmin Chen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Valerie Collij
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marjiolein A Y Klaassen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Laura A Bolte
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Milla F Brandao Gois
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Pieter B T Neerincx
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | | | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | - Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. .,Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Cagliari, Italy.
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13
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Gacesa R, Kurilshikov A, Vich Vila A, Sinha T, Klaassen MAY, Bolte LA, Andreu-Sánchez S, Chen L, Collij V, Hu S, Dekens JAM, Lenters VC, Björk JR, Swarte JC, Swertz MA, Jansen BH, Gelderloos-Arends J, Jankipersadsing S, Hofker M, Vermeulen RCH, Sanna S, Harmsen HJM, Wijmenga C, Fu J, Zhernakova A, Weersma RK. Environmental factors shaping the gut microbiome in a Dutch population. Nature 2022; 604:732-739. [PMID: 35418674 DOI: 10.1038/s41586-022-04567-7] [Citation(s) in RCA: 198] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/18/2022] [Indexed: 12/22/2022]
Abstract
The gut microbiome is associated with diverse diseases1-3, but a universal signature of a healthy or unhealthy microbiome has not been identified, and there is a need to understand how genetics, exposome, lifestyle and diet shape the microbiome in health and disease. Here we profiled bacterial composition, function, antibiotic resistance and virulence factors in the gut microbiomes of 8,208 Dutch individuals from a three-generational cohort comprising 2,756 families. We correlated these to 241 host and environmental factors, including physical and mental health, use of medication, diet, socioeconomic factors and childhood and current exposome. We identify that the microbiome is shaped primarily by the environment and cohabitation. Only around 6.6% of taxa are heritable, whereas the variance of around 48.6% of taxa is significantly explained by cohabitation. By identifying 2,856 associations between the microbiome and health, we find that seemingly unrelated diseases share a common microbiome signature that is independent of comorbidities. Furthermore, we identify 7,519 associations between microbiome features and diet, socioeconomics and early life and current exposome, with numerous early-life and current factors being significantly associated with microbiome function and composition. Overall, this study provides a comprehensive overview of gut microbiome and the underlying impact of heritability and exposures that will facilitate future development of microbiome-targeted therapies.
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Affiliation(s)
- R Gacesa
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - A Kurilshikov
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - A Vich Vila
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - T Sinha
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - M A Y Klaassen
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - L A Bolte
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - S Andreu-Sánchez
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - L Chen
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - V Collij
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - S Hu
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - J A M Dekens
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,Center of Development and Innovation, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - V C Lenters
- University Medical Centre Utrecht, Julius Center for Health Sciences and Primary Care, Utrecht, The Netherlands
| | - J R Björk
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - J C Swarte
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - M A Swertz
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
| | - B H Jansen
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - J Gelderloos-Arends
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - S Jankipersadsing
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - M Hofker
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - R C H Vermeulen
- University Medical Centre Utrecht, Julius Center for Health Sciences and Primary Care, Utrecht, The Netherlands.,Utrecht University, Institute for Risk Assessment Sciences (IRAS), Department of Population Health Sciences, Utrecht, The Netherlands
| | - S Sanna
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Cagliari, Italy
| | - H J M Harmsen
- Department of Medical Microbiology and Infection prevention, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - C Wijmenga
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - J Fu
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands. .,Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.
| | - A Zhernakova
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
| | - R K Weersma
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.
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14
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Le Roy CI, Kurilshikov A, Leeming ER, Visconti A, Bowyer RCE, Menni C, Fachi M, Koutnikova H, Veiga P, Zhernakova A, Derrien M, Spector TD. Correction to: Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome. BMC Microbiol 2022; 22:66. [PMID: 35227199 PMCID: PMC8883623 DOI: 10.1186/s12866-022-02482-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Caroline Ivanne Le Roy
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Emily R Leeming
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Alessia Visconti
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Ruth C E Bowyer
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Cristina Menni
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Mario Fachi
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | | | | | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK.
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15
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Le Roy CI, Kurilshikov A, Leeming ER, Visconti A, Bowyer RCE, Menni C, Fachi M, Koutnikova H, Veiga P, Zhernakova A, Derrien M, Spector TD. Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome. BMC Microbiol 2022; 22:39. [PMID: 35114943 PMCID: PMC8812230 DOI: 10.1186/s12866-021-02364-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 10/18/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Yoghurt contains live bacteria that could contribute via modulation of the gut microbiota to its reported beneficial effects such as reduced body weight gain and lower incidence of type 2 diabetes. To date, the association between yoghurt consumption and the composition of the gut microbiota is underexplored. Here we used clinical variables, metabolomics, 16S rRNA and shotgun metagenomic sequencing data collected on over 1000 predominantly female UK twins to define the link between the gut microbiota and yoghurt-associated health benefits. RESULTS According to food frequency questionnaires (FFQ), 73% of subjects consumed yoghurt. Consumers presented a healthier diet pattern (healthy eating index: beta = 2.17 ± 0.34; P = 2.72x10-10) and improved metabolic health characterised by reduced visceral fat (beta = -28.18 ± 11.71 g; P = 0.01). According to 16S rRNA gene analyses and whole shotgun metagenomic sequencing approach consistent taxonomic variations were observed with yoghurt consumption. More specifically, we identified higher abundance of species used as yoghurt starters Streptococcus thermophilus (beta = 0.41 ± 0.051; P = 6.14x10-12) and sometimes added Bifidobacterium animalis subsp. lactis (beta = 0.30 ± 0.052; P = 1.49x10-8) in the gut of yoghurt consumers. Replication in 1103 volunteers from the LifeLines-DEEP cohort confirmed the increase of S. thermophilus among yoghurt consumers. Using food records collected the day prior to faecal sampling we showed than an increase in these two yoghurt bacteria could be transient. Metabolomics analysis revealed that B. animalis subsp. lactis was associated with 13 faecal metabolites including a 3-hydroxyoctanoic acid, known to be involved in the regulation of gut inflammation. CONCLUSIONS Yoghurt consumption is associated with reduced visceral fat mass and changes in gut microbiome including transient increase of yoghurt-contained species (i.e. S. thermophilus and B. lactis).
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Affiliation(s)
- Caroline Ivanne Le Roy
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, SE1 7EH UK
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Emily R. Leeming
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, SE1 7EH UK
| | - Alessia Visconti
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, SE1 7EH UK
| | - Ruth C. E. Bowyer
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, SE1 7EH UK
| | - Cristina Menni
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, SE1 7EH UK
| | - Mario Fachi
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, SE1 7EH UK
| | | | | | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Tim D. Spector
- Department of Twin Research & Genetic Epidemiology, King’s College London, London, SE1 7EH UK
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16
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Sanna S, Kurilshikov A, van der Graaf A, Fu J, Zhernakova A. Challenges and future directions for studying effects of host genetics on the gut microbiome. Nat Genet 2022; 54:100-106. [PMID: 35115688 DOI: 10.1038/s41588-021-00983-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/02/2021] [Indexed: 12/15/2022]
Abstract
The human gut microbiome is a complex ecosystem that is involved in its host's metabolism, immunity and health. Although interindividual variations in gut microbial composition are mainly driven by environmental factors, some gut microorganisms are heritable and thus can be influenced by host genetics. In the past 5 years, 12 microbial genome-wide association studies (mbGWAS) with >1,000 participants have been published, yet only a few genetic loci have been consistently confirmed across multiple studies. Here we discuss the state of the art for mbGWAS, focusing on current challenges such as the heterogeneity of microbiome measurements and power issues, and we elaborate on potential future directions for genetic analysis of the microbiome.
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Affiliation(s)
- Serena Sanna
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Monserrato, Cagliari, Italy.
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Adriaan van der Graaf
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Jingyuan Fu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.
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17
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Lopera-Maya EA, Kurilshikov A, van der Graaf A, Hu S, Andreu-Sánchez S, Chen L, Vila AV, Gacesa R, Sinha T, Collij V, Klaassen MAY, Bolte LA, Gois MFB, Neerincx PBT, Swertz MA, Harmsen HJM, Wijmenga C, Fu J, Weersma RK, Zhernakova A, Sanna S. Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project. Nat Genet 2022; 54:143-151. [PMID: 35115690 DOI: 10.1038/s41588-021-00992-y] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 11/19/2021] [Indexed: 02/07/2023]
Abstract
Host genetics are known to influence the gut microbiome, yet their role remains poorly understood. To robustly characterize these effects, we performed a genome-wide association study of 207 taxa and 205 pathways representing microbial composition and function in 7,738 participants of the Dutch Microbiome Project. Two robust, study-wide significant (P < 1.89 × 10-10) signals near the LCT and ABO genes were found to be associated with multiple microbial taxa and pathways and were replicated in two independent cohorts. The LCT locus associations seemed modulated by lactose intake, whereas those at ABO could be explained by participant secretor status determined by their FUT2 genotype. Twenty-two other loci showed suggestive evidence (P < 5 × 10-8) of association with microbial taxa and pathways. At a more lenient threshold, the number of loci we identified strongly correlated with trait heritability, suggesting that much larger sample sizes are needed to elucidate the remaining effects of host genetics on the gut microbiome.
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Affiliation(s)
- Esteban A Lopera-Maya
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adriaan van der Graaf
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shixian Hu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lianmin Chen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Valerie Collij
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marjiolein A Y Klaassen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Laura A Bolte
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Milla F Brandao Gois
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Pieter B T Neerincx
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | - Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Cagliari, Italy.
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18
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Gulyaeva A, Garmaeva S, Ruigrok RAAA, Wang D, Riksen NP, Netea MG, Wijmenga C, Weersma RK, Fu J, Vila AV, Kurilshikov A, Zhernakova A. Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts. Cell Rep 2022; 38:110204. [PMID: 35021085 DOI: 10.1016/j.celrep.2021.110204] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/03/2021] [Accepted: 12/13/2021] [Indexed: 12/16/2022] Open
Abstract
The crAss-like phages are a diverse group of related viruses that includes some of the most abundant viruses of the human gut. To explore their diversity and functional role in human population and clinical cohorts, we analyze gut metagenomic data collected from 1,950 individuals from the Netherlands. We identify 1,556 crAss-like phage genomes, including 125 species-level and 32 genus-level clusters absent from the reference databases used. Analysis of their genomic features shows that closely related crAss-like phages can possess strikingly divergent regions responsible for transcription, presumably acquired through recombination. Prediction of crAss-like phage hosts points primarily to bacteria of the phylum Bacteroidetes, consistent with previous reports. Finally, we explore the temporal stability of crAss-like phages over a 4-year period and identify associations between the abundance of crAss-like phages and several human phenotypes, including depletion of crAss-like phages in inflammatory bowel disease patients.
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Affiliation(s)
- Anastasia Gulyaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands.
| | - Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Renate A A A Ruigrok
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Daoming Wang
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Niels P Riksen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen 6525GA, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen 6525GA, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Rinse K Weersma
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands.
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19
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Mujagic Z, Kasapi M, Jonkers DMAE, Garcia-Perez I, Vork L, Weerts ZZR, Serrano-Contreras JI, Zhernakova A, Kurilshikov A, Scotcher J, Holmes E, Wijmenga C, Keszthelyi D, Nicholson JK, Posma JM, Masclee AAM. Integrated fecal microbiome-metabolome signatures reflect stress and serotonin metabolism in irritable bowel syndrome. Gut Microbes 2022; 14:2063016. [PMID: 35446234 PMCID: PMC9037519 DOI: 10.1080/19490976.2022.2063016] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
To gain insight into the complex microbiome-gut-brain axis in irritable bowel syndrome (IBS), several modalities of biological and clinical data must be combined. We aimed to identify profiles of fecal microbiota and metabolites associated with IBS and to delineate specific phenotypes of IBS that represent potential pathophysiological mechanisms. Fecal metabolites were measured using proton nuclear magnetic resonance (1H-NMR) spectroscopy and gut microbiome using shotgun metagenomic sequencing (MGS) in a combined dataset of 142 IBS patients and 120 healthy controls (HCs) with extensive clinical, biological and phenotype information. Data were analyzed using support vector classification and regression and kernel t-SNE. Microbiome and metabolome profiles could distinguish IBS and HC with an area-under-the-receiver-operator-curve of 77.3% and 79.5%, respectively, but this could be improved by combining microbiota and metabolites to 83.6%. No significant differences in predictive ability of the microbiome-metabolome data were observed between the three classical, stool pattern-based, IBS subtypes. However, unsupervised clustering showed distinct subsets of IBS patients based on fecal microbiome-metabolome data. These clusters could be related plasma levels of serotonin and its metabolite 5-hydroxyindoleacetate, effects of psychological stress on gastrointestinal (GI) symptoms, onset of IBS after stressful events, medical history of previous abdominal surgery, dietary caloric intake and IBS symptom duration. Furthermore, pathways in metabolic reaction networks were integrated with microbiota data, that reflect the host-microbiome interactions in IBS. The identified microbiome-metabolome signatures for IBS, associated with altered serotonin metabolism and unfavorable stress response related to GI symptoms, support the microbiota-gut-brain link in the pathogenesis of IBS.
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Affiliation(s)
- Zlatan Mujagic
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands,Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, South Kensington Campus, Imperial College London, London, UK,CONTACT Zlatan Mujagic Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Melpomeni Kasapi
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, South Kensington Campus, Imperial College London, London, UK
| | - Daisy MAE Jonkers
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Isabel Garcia-Perez
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Hammersmith Campus, Imperial College London, London, UK
| | - Lisa Vork
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Zsa Zsa R.M. Weerts
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Jose Ivan Serrano-Contreras
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, South Kensington Campus, Imperial College London, London, UK
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jamie Scotcher
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, South Kensington Campus, Imperial College London, London, UK
| | - Elaine Holmes
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Hammersmith Campus, Imperial College London, London, UK,The Australian National Phenome Center, Harry Perkins Institute, Murdoch University, Perth, Australia
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Daniel Keszthelyi
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Jeremy K Nicholson
- The Australian National Phenome Center, Harry Perkins Institute, Murdoch University, Perth, Australia
| | - Joram M Posma
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, South Kensington Campus, Imperial College London, London, UK
| | - Ad AM Masclee
- Division Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands,Nutrim School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
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20
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Brandao Gois MF, Sinha T, Spreckels JE, Vich Vila A, Bolte LA, Weersma RK, Wijmenga C, Fu J, Zhernakova A, Kurilshikov A. Role of the gut microbiome in mediating lactose intolerance symptoms. Gut 2022; 71:215-217. [PMID: 34086598 PMCID: PMC8666824 DOI: 10.1136/gutjnl-2020-323911] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/13/2021] [Accepted: 02/22/2021] [Indexed: 12/19/2022]
Affiliation(s)
- M F Brandao Gois
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Trishla Sinha
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Johanne E Spreckels
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands,Department of Gastroenterology and Hepatology, University Medical Centre Groningen, Groningen, The Netherlands
| | - Laura A Bolte
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands,Department of Gastroenterology and Hepatology, University Medical Centre Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University Medical Centre Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands,Department of Pediatrics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
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21
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Gacesa R, Vich Vila A, Collij V, Mujagic Z, Kurilshikov A, Voskuil M, Festen E, Wijmenga C, Jonkers D, Dijkstra G, Fu J, Zhernakova A, Imhann F, Weersma R. A combination of fecal calprotectin and human beta-defensin 2 facilitates diagnosis and monitoring of inflammatory bowel disease. Gut Microbes 2021; 13:1943288. [PMID: 34313538 PMCID: PMC8317932 DOI: 10.1080/19490976.2021.1943288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) show a large overlap in clinical presentation, which presents diagnostic challenges. As a consequence, invasive and burdensome endoscopies are often used to distinguish between IBD and IBS. Here, we aimed to develop a noninvasive fecal test that can distinguish between IBD and IBS and reduce the number of endoscopies.We used shotgun metagenomic sequencing to analyze the composition and function of gut microbiota of 169 IBS patients, 447 IBD patients and 1044 population controls and measured fecal Calprotectin (FCal), human beta defensin 2 (HBD2), and chromogranin A (CgA) in these samples. These measurements were used to construct training sets (75% of data) for logistic regression and machine learning models to differentiate IBS from IBD and inactive from active IBD. The results were replicated on test sets (remaining 25% of the data) and microbiome data obtained using 16S sequencing.Fecal HBD2 showed high sensitivity and specificity for differentiating between IBD and IBS (sensitivity = 0.89, specificity = 0.76), while the inclusion of microbiome data with biomarkers (HBD2 and FCal) showed a potential for improvement in predictive power (optimal sensitivity = 0.87, specificity = 0.93). Shotgun sequencing-based models produced comparable results using 16S-sequencing data. HBD2 and FCal were found to have predictive power for IBD disease activity (AUC ≈ 0.7).HBD2 is a novel biomarker for IBD in patients with gastro-intestinal complaints, especially when used in combination with FCal and potentially in combination with gut microbiome data.
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Affiliation(s)
- R. Gacesa
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - A. Vich Vila
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - V. Collij
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Z. Mujagic
- Maastricht University Medical Center, Division of Gastroenterology-Hepatology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht, The Netherlands
| | - A. Kurilshikov
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - M.D. Voskuil
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - E.A.M. Festen
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - C. Wijmenga
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - D.M.A.E. Jonkers
- Maastricht University Medical Center, Division of Gastroenterology-Hepatology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht, The Netherlands
| | - G. Dijkstra
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - J. Fu
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University of Groningen and University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - A. Zhernakova
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - F. Imhann
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands,CONTACT F. Imhann University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - R.K. Weersma
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
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22
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Bonfiglio F, Liu X, Smillie C, Pandit A, Kurilshikov A, Bacigalupe R, Zheng T, Nim H, Garcia-Etxebarria K, Bujanda L, Andreasson A, Agreus L, Walter S, Abecasis G, Eijsbouts C, Jostins L, Parkes M, Hughes DA, Timpson N, Raes J, Franke A, Kennedy NA, Regev A, Zhernakova A, Simren M, Camilleri M, D'Amato M. GWAS of stool frequency provides insights into gastrointestinal motility and irritable bowel syndrome. Cell Genom 2021; 1:None. [PMID: 34957435 PMCID: PMC8654685 DOI: 10.1016/j.xgen.2021.100069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 07/27/2021] [Accepted: 10/11/2021] [Indexed: 02/07/2023]
Abstract
Gut dysmotility is associated with constipation, diarrhea, and functional gastrointestinal disorders like irritable bowel syndrome (IBS), although its molecular underpinnings are poorly characterized. We studied stool frequency (defined by the number of bowel movements per day, based on questionnaire data) as a proxy for gut motility in a GWAS meta-analysis including 167,875 individuals from UK Biobank and four smaller population-based cohorts. We identify 14 loci associated with stool frequency (p ≤ 5.0 × 10-8). Gene set and pathway analyses detected enrichment for genes involved in neurotransmitter/neuropeptide signaling and preferentially expressed in enteric motor neurons controlling peristalsis. PheWAS identified pleiotropic associations with dysmotility syndromes and the response to their pharmacological treatment. The genetic architecture of stool frequency correlates with that of IBS, and UK Biobank participants from the top 1% of stool frequency polygenic score distribution were associated with 5× higher risk of IBS with diarrhea. These findings pave the way for the identification of actionable pathological mechanisms in IBS and the dysmotility syndromes.
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Affiliation(s)
- Ferdinando Bonfiglio
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.,Unit of Clinical Epidemiology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Xingrong Liu
- Unit of Clinical Epidemiology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Anita Pandit
- Department of Biostatistics, University of Michigan, School of Public Health, Ann Arbor, MI, USA
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rodrigo Bacigalupe
- Department of Microbiology and Immunology, Rega Instituut, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven 3000, Belgium
| | - Tenghao Zheng
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.,Unit of Clinical Epidemiology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Hieu Nim
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | | | - Luis Bujanda
- Department of Gastrointestinal and Liver Diseases, Biodonostia HRI, San Sebastian, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain.,Universidad del País Vasco (UPV/EHU), San Sebastian, Spain
| | - Anna Andreasson
- Division of Clinical Medicine, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Lars Agreus
- Division of Family Medicine and Primary Care, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Susanna Walter
- Division of Neuro and Inflammation Science, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Gonçalo Abecasis
- Department of Biostatistics, University of Michigan, School of Public Health, Ann Arbor, MI, USA
| | - Chris Eijsbouts
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Luke Jostins
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.,Christ Church, University of Oxford, Oxford, UK
| | - Miles Parkes
- Division of Gastroenterology, Department of Medicine, University of Cambridge, Cambridge, UK
| | - David A Hughes
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Nicholas Timpson
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Instituut, KU Leuven, Leuven, Belgium.,Center for Microbiology, VIB, Leuven 3000, Belgium
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Nicholas A Kennedy
- IBD Pharmacogenetics, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute, Cambridge, MA, USA
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Magnus Simren
- Dept of Internal Medicine & Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Michael Camilleri
- Clinical Enteric Neuroscience Translational and Epidemiological Research (CENTER) and Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Mauro D'Amato
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.,Unit of Clinical Epidemiology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.,Department of Gastrointestinal and Liver Diseases, Biodonostia HRI, San Sebastian, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.,Gastrointestinal Genetics Lab, CIC bioGUNE - BRTA, Derio, Spain
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23
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Freidin MB, Stalteri MA, Wells PM, Lachance G, Baleanu AF, Bowyer RCE, Kurilshikov A, Zhernakova A, Steves CJ, Williams FMK. An association between chronic widespread pain and the gut microbiome. Rheumatology (Oxford) 2021; 60:3727-3737. [PMID: 33331911 PMCID: PMC8328510 DOI: 10.1093/rheumatology/keaa847] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 11/12/2020] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVES Chronic widespread musculoskeletal pain (CWP) is a characteristic symptom of fibromyalgia, which has been shown to be associated with an altered gut microbiome. Microbiome studies to date have not examined the milder CWP phenotype specifically nor have they explored the role of raised BMI. The aim of this study was to investigate whether the microbiome is abnormal in CWP. METHODS CWP was assessed using a standardized screening questionnaire in female volunteers from the TwinsUK cohort including 113 CWP cases and 1623 controls. The stool microbiome was characterized using 16S rRNA amplicon sequencing and amplicon sequence variants, and associations with CWP examined using linear mixed-effects models adjusting for BMI, age, diet, family relatedness and technical factors. RESULTS Alpha diversity was significantly lower in CWP cases than controls (Mann-Whitney test, P-values 2.3e-04 and 1.2e-02, for Shannon and Simpson indices respectively). The species Coprococcus comes was significantly depleted in CWP cases (Padj = 3.04e-03). A genome-wide association study (GWAS) performed for C. comes in TwinsUK followed by meta-analysis with three Dutch cohorts (total n = 3521) resulted in nine suggestive regions, with the most convincing on chromosome 4 near the TRAM1L1 gene (rs76957229, P = 7.4e-8). A Mendelian randomization study based on the results of the GWAS did not support a causal role for C. comes on the development of CWP. CONCLUSIONS We have demonstrated reduced diversity in the microbiome in CWP, indicating an involvement of the gut microbiota in CWP; prospectively the microbiome may offer therapeutic opportunities for this condition.
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Affiliation(s)
- Maxim B Freidin
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Maria A Stalteri
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Philippa M Wells
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Genevieve Lachance
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Andrei-Florin Baleanu
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Ruth C E Bowyer
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
| | - Frances M K Williams
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London, UK
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24
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Chen Z, Radjabzadeh D, Chen L, Kurilshikov A, Kavousi M, Ahmadizar F, Ikram MA, Uitterlinden AG, Zhernakova A, Fu J, Kraaij R, Voortman T. Association of Insulin Resistance and Type 2 Diabetes With Gut Microbial Diversity: A Microbiome-Wide Analysis From Population Studies. JAMA Netw Open 2021; 4:e2118811. [PMID: 34323983 PMCID: PMC8322996 DOI: 10.1001/jamanetworkopen.2021.18811] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
IMPORTANCE Previous studies have indicated that gut microbiome may be associated with development of type 2 diabetes. However, these studies are limited by small sample size and insufficient for confounding. Furthermore, which specific taxa play a role in the development of type 2 diabetes remains unclear. OBJECTIVE To examine associations of gut microbiome composition with insulin resistance and type 2 diabetes in a large population-based setting controlling for various sociodemographic and lifestyle factors. DESIGN, SETTING, AND PARTICIPANTS This cross-sectional analysis included 2166 participants from 2 Dutch population-based prospective cohorts: the Rotterdam Study and the LifeLines-DEEP study. EXPOSURES The 16S ribosomal RNA method was used to measure microbiome composition in stool samples collected between January 1, 2012, and December 31, 2013. The α diversity (Shannon, richness, and Inverse Simpson indexes), β diversity (Bray-Curtis dissimilarity matrix), and taxa (from domain to genus level) were identified to reflect gut microbiome composition. MAIN OUTCOMES AND MEASURES Associations among α diversity, β diversity, and taxa with the Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) and with type 2 diabetes were examined. Glucose and insulin were measured to calculate the HOMA-IR. Type 2 diabetes cases were identified based on glucose levels and medical records from January 2012 to December 2013. Analyses were adjusted for technical covariates, lifestyle, sociodemographic, and medical factors. Data analysis was performed from January 1, 2018, to December 31, 2020. RESULTS There were 2166 participants in this study: 1418 from the Rotterdam Study (mean [SD] age, 62.4 [5.9] years; 815 [57.5%] male) and 748 from the LifeLines-DEEP study (mean [SD] age, 44.7 [13.4] years; 431 [57.6%] male); from this total, 193 type 2 diabetes cases were identified. Lower microbiome Shannon index and richness were associated with higher HOMA-IR (eg, Shannon index, -0.06; 95% CI, -0.10 to -0.02), and patients with type 2 diabetes had a lower richness than participants without diabetes (odds ratio [OR], 0.93; 95% CI, 0.88-0.99). The β diversity (Bray-Curtis dissimilarity matrix) was associated with insulin resistance (R2 = 0.004, P = .001 in the Rotterdam Study and R2 = 0.005, P = .002 in the LifeLines-DEEP study). A total of 12 groups of bacteria were associated with HOMA-IR or type 2 diabetes. Specifically, a higher abundance of Christensenellaceae (β = -0.08; 95% CI, -0.12 to -0.03: P < .001), Christensenellaceae R7 group (β = -0.07; 95% CI, -0.12 to -0.03; P < .001), Marvinbryantia (β = -0.07; 95% CI, -0.11 to -0.03; P < .001), Ruminococcaceae UCG005 (β = -0.09; 95% CI, -0.13 to -0.05; P < .001), Ruminococcaceae UCG008 (β = -0.07; 95% CI, -0.11 to -0.03; P < .001), Ruminococcaceae UCG010 (β = -0.08; 95% CI, -0.12 to -0.04; P < .001), or Ruminococcaceae NK4A214 group (β = -0.09; 95% CI, -0.13 to -0.05; P < .001) was associated with lower HOMA-IR. A higher abundance of Clostridiaceae 1 (OR, 0.51; 95% CI, 0.41-0.65; P < .001), Peptostreptococcaceae (OR, 0.56; 95% CI, 0.45-0.70; P < .001), C sensu stricto 1 (OR, 0.51; 95% CI, 0.40-0.65; P < .001), Intestinibacter (OR, 0.60; 95% CI, 0.48-0.76; P < .001), or Romboutsia (OR, 0.55; 95% CI, 0.44-0.70; P < .001) was associated with less type 2 diabetes. These bacteria are all known to produce butyrate. CONCLUSIONS AND RELEVANCE In this cross-sectional study, higher microbiome α diversity, along with more butyrate-producing gut bacteria, was associated with less type 2 diabetes and with lower insulin resistance among individuals without diabetes. These findings could help provide insight into the etiology, pathogenesis, and treatment of type 2 diabetes.
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Affiliation(s)
- Zhangling Chen
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Lianmin Chen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Cardiology, Nanjing Medical University, The First Affiliated Hospital of Nanjing Medical University, Nanjing
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Fariba Ahmadizar
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Andre G. Uitterlinden
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
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25
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Bolte LA, Vich Vila A, Imhann F, Collij V, Gacesa R, Peters V, Wijmenga C, Kurilshikov A, Campmans-Kuijpers MJE, Fu J, Dijkstra G, Zhernakova A, Weersma RK. Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome. Gut 2021; 70:1287-1298. [PMID: 33811041 PMCID: PMC8223641 DOI: 10.1136/gutjnl-2020-322670] [Citation(s) in RCA: 214] [Impact Index Per Article: 71.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The microbiome directly affects the balance of pro-inflammatory and anti-inflammatory responses in the gut. As microbes thrive on dietary substrates, the question arises whether we can nourish an anti-inflammatory gut ecosystem. We aim to unravel interactions between diet, gut microbiota and their functional ability to induce intestinal inflammation. DESIGN We investigated the relation between 173 dietary factors and the microbiome of 1425 individuals spanning four cohorts: Crohn's disease, ulcerative colitis, irritable bowel syndrome and the general population. Shotgun metagenomic sequencing was performed to profile gut microbial composition and function. Dietary intake was assessed through food frequency questionnaires. We performed unsupervised clustering to identify dietary patterns and microbial clusters. Associations between diet and microbial features were explored per cohort, followed by a meta-analysis and heterogeneity estimation. RESULTS We identified 38 associations between dietary patterns and microbial clusters. Moreover, 61 individual foods and nutrients were associated with 61 species and 249 metabolic pathways in the meta-analysis across healthy individuals and patients with IBS, Crohn's disease and UC (false discovery rate<0.05). Processed foods and animal-derived foods were consistently associated with higher abundances of Firmicutes, Ruminococcus species of the Blautia genus and endotoxin synthesis pathways. The opposite was found for plant foods and fish, which were positively associated with short-chain fatty acid-producing commensals and pathways of nutrient metabolism. CONCLUSION We identified dietary patterns that consistently correlate with groups of bacteria with shared functional roles in both, health and disease. Moreover, specific foods and nutrients were associated with species known to infer mucosal protection and anti-inflammatory effects. We propose microbial mechanisms through which the diet affects inflammatory responses in the gut as a rationale for future intervention studies.
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Affiliation(s)
- Laura A Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Valerie Collij
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Vera Peters
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Marjo J E Campmans-Kuijpers
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
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26
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Garmaeva S, Gulyaeva A, Sinha T, Shkoporov AN, Clooney AG, Stockdale SR, Spreckels JE, Sutton TDS, Draper LA, Dutilh BE, Wijmenga C, Kurilshikov A, Fu J, Hill C, Zhernakova A. Stability of the human gut virome and effect of gluten-free diet. Cell Rep 2021; 35:109132. [PMID: 34010651 DOI: 10.1016/j.celrep.2021.109132] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 01/12/2021] [Accepted: 04/23/2021] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiome consists of bacteria, archaea, eukaryotes, and viruses. The gut viruses are relatively underexplored. Here, we longitudinally analyzed the gut virome composition in 11 healthy adults: its stability, variation, and the effect of a gluten-free diet. Using viral enrichment and a de novo assembly-based approach, we demonstrate the quantitative dynamics of the gut virome, including dsDNA, ssDNA, dsRNA, and ssRNA viruses. We observe highly divergent individual viral communities, carrying on an average 2,143 viral genomes, 13.1% of which were present at all 3 time points. In contrast to previous reports, the Siphoviridae family dominates over Microviridae in studied individual viromes. We also show individual viromes to be stable at the family level but to vary substantially at the genera and species levels. Finally, we demonstrate that lower initial diversity of the human gut virome leads to a more pronounced effect of the dietary intervention on its composition.
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Affiliation(s)
- Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Anastasia Gulyaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Andrey N Shkoporov
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Adam G Clooney
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Stephen R Stockdale
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Johanne E Spreckels
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Thomas D S Sutton
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Lorraine A Draper
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht 3584 CH, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands
| | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713GZ, the Netherlands.
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Hu S, Vich Vila A, Gacesa R, Collij V, Stevens C, Fu JM, Wong I, Talkowski ME, Rivas MA, Imhann F, Bolte L, van Dullemen H, Dijkstra G, Visschedijk MC, Festen EA, Xavier RJ, Fu J, Daly MJ, Wijmenga C, Zhernakova A, Kurilshikov A, Weersma RK. Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD. Gut 2021; 70:285-296. [PMID: 32651235 PMCID: PMC7815889 DOI: 10.1136/gutjnl-2019-319706] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 04/08/2020] [Accepted: 04/20/2020] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Both the gut microbiome and host genetics are known to play significant roles in the pathogenesis of IBD. However, the interaction between these two factors and its implications in the aetiology of IBD remain underexplored. Here, we report on the influence of host genetics on the gut microbiome in IBD. DESIGN To evaluate the impact of host genetics on the gut microbiota of patients with IBD, we combined whole exome sequencing of the host genome and whole genome shotgun sequencing of 1464 faecal samples from 525 patients with IBD and 939 population-based controls. We followed a four-step analysis: (1) exome-wide microbial quantitative trait loci (mbQTL) analyses, (2) a targeted approach focusing on IBD-associated genomic regions and protein truncating variants (PTVs, minor allele frequency (MAF) >5%), (3) gene-based burden tests on PTVs with MAF <5% and exome copy number variations (CNVs) with site frequency <1%, (4) joint analysis of both cohorts to identify the interactions between disease and host genetics. RESULTS We identified 12 mbQTLs, including variants in the IBD-associated genes IL17REL, MYRF, SEC16A and WDR78. For example, the decrease of the pathway acetyl-coenzyme A biosynthesis, which is involved in short chain fatty acids production, was associated with variants in the gene MYRF (false discovery rate <0.05). Changes in functional pathways involved in the metabolic potential were also observed in participants carrying rare PTVs or CNVs in CYP2D6, GPR151 and CD160 genes. These genes are known for their function in the immune system. Moreover, interaction analyses confirmed previously known IBD disease-specific mbQTLs in TNFSF15. CONCLUSION This study highlights that both common and rare genetic variants affecting the immune system are key factors in shaping the gut microbiota in the context of IBD and pinpoints towards potential mechanisms for disease treatment.
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Affiliation(s)
- Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Valerie Collij
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Christine Stevens
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jack M Fu
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Isaac Wong
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Michael E Talkowski
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Manuel A Rivas
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Laura Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Hendrik van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Marijn C Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Eleonora A Festen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Ramnik J Xavier
- Center for Microbiome Informatics and Therapeutic, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Jingyuan Fu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Mark J Daly
- Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
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Kurilshikov A, Medina-Gomez C, Bacigalupe R, Radjabzadeh D, Wang J, Demirkan A, Le Roy CI, Raygoza Garay JA, Finnicum CT, Liu X, Zhernakova DV, Bonder MJ, Hansen TH, Frost F, Rühlemann MC, Turpin W, Moon JY, Kim HN, Lüll K, Barkan E, Shah SA, Fornage M, Szopinska-Tokov J, Wallen ZD, Borisevich D, Agreus L, Andreasson A, Bang C, Bedrani L, Bell JT, Bisgaard H, Boehnke M, Boomsma DI, Burk RD, Claringbould A, Croitoru K, Davies GE, van Duijn CM, Duijts L, Falony G, Fu J, van der Graaf A, Hansen T, Homuth G, Hughes DA, Ijzerman RG, Jackson MA, Jaddoe VWV, Joossens M, Jørgensen T, Keszthelyi D, Knight R, Laakso M, Laudes M, Launer LJ, Lieb W, Lusis AJ, Masclee AAM, Moll HA, Mujagic Z, Qibin Q, Rothschild D, Shin H, Sørensen SJ, Steves CJ, Thorsen J, Timpson NJ, Tito RY, Vieira-Silva S, Völker U, Völzke H, Võsa U, Wade KH, Walter S, Watanabe K, Weiss S, Weiss FU, Weissbrod O, Westra HJ, Willemsen G, Payami H, Jonkers DMAE, Arias Vasquez A, de Geus EJC, Meyer KA, Stokholm J, Segal E, Org E, Wijmenga C, Kim HL, Kaplan RC, Spector TD, Uitterlinden AG, Rivadeneira F, Franke A, Lerch MM, Franke L, Sanna S, D'Amato M, Pedersen O, Paterson AD, Kraaij R, Raes J, Zhernakova A. Large-scale association analyses identify host factors influencing human gut microbiome composition. Nat Genet 2021; 53:156-165. [PMID: 33462485 PMCID: PMC8515199 DOI: 10.1038/s41588-020-00763-1] [Citation(s) in RCA: 541] [Impact Index Per Article: 180.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 12/14/2020] [Indexed: 01/29/2023]
Abstract
To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts). Microbial composition showed high variability across cohorts: only 9 of 410 genera were detected in more than 95% of samples. A genome-wide association study of host genetic variation regarding microbial taxa identified 31 loci affecting the microbiome at a genome-wide significant (P < 5 × 10-8) threshold. One locus, the lactase (LCT) gene locus, reached study-wide significance (genome-wide association study signal: P = 1.28 × 10-20), and it showed an age-dependent association with Bifidobacterium abundance. Other associations were suggestive (1.95 × 10-10 < P < 5 × 10-8) but enriched for taxa showing high heritability and for genes expressed in the intestine and brain. A phenome-wide association study and Mendelian randomization identified enrichment of microbiome trait loci in the metabolic, nutrition and environment domains and suggested the microbiome might have causal effects in ulcerative colitis and rheumatoid arthritis.
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Affiliation(s)
- Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Rodrigo Bacigalupe
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Jun Wang
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ayse Demirkan
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Section of Statistical Multi-Omics, Department of Clinical & Experimental Medicine, School of Biosciences & Medicine, University of Surrey, Guildford, UK
| | - Caroline I Le Roy
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Juan Antonio Raygoza Garay
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Casey T Finnicum
- Avera Institute of Human Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD, USA
| | - Xingrong Liu
- Center for Molecular Medicine and Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Daria V Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO University, St. Petersburg, Russia
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tue H Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fabian Frost
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Malte C Rühlemann
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Williams Turpin
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Han-Na Kim
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Clinical Research Design and Evaluation, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Kreete Lüll
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Elad Barkan
- Department of Computer Science and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shiraz A Shah
- COPSAC, Copenhagen University Hospital, Copenhagen, Denmark
| | - Myriam Fornage
- Institute of Molecular Medicine McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Joanna Szopinska-Tokov
- Department of Psychiatry, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Zachary D Wallen
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dmitrii Borisevich
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Agreus
- Division of Family Medicine and Primary Care, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Anna Andreasson
- Stress Research Institute, Stockholm University, Stockholm, Sweden
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Larbi Bedrani
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Hans Bisgaard
- COPSAC, Copenhagen University Hospital, Copenhagen, Denmark
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Dorret I Boomsma
- Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Robert D Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Annique Claringbould
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Kenneth Croitoru
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Gareth E Davies
- Avera Institute of Human Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD, USA
- Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Liesbeth Duijts
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Gwen Falony
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adriaan van der Graaf
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - David A Hughes
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Richard G Ijzerman
- Department of Endocrinology, Amsterdam University Medical Center, location VUMC, Amsterdam, the Netherlands
| | - Matthew A Jackson
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Vincent W V Jaddoe
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Marie Joossens
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Torben Jørgensen
- Centre for Clinical Research and Prevention, Bispebjerg/Frederiksberg Hospital, Capital Region of Copenhagen and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Daniel Keszthelyi
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, the Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation and Department of Bioengeering, University of California, San Diego, La Jolla, CA, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Matthias Laudes
- Department of Medicine I, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Science, National Institute on Aging, Bethesda, MD, USA
| | - Wolfgang Lieb
- Institute of Epidemiology, Kiel University, Kiel, Germany
| | - Aldons J Lusis
- Departments of Microbiology, Immunology and Molecular Genetics, and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ad A M Masclee
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, the Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Henriette A Moll
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Zlatan Mujagic
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, the Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Qi Qibin
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Daphna Rothschild
- Department of Computer Science and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hocheol Shin
- Department of Family Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Claire J Steves
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | | | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Raul Y Tito
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Sara Vieira-Silva
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Urmo Võsa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Kaitlin H Wade
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Susanna Walter
- Department of Biomedical and Clinical Sciences, University of Linköping, Linköping, Sweden
- Department of Gastroenterology, County Council of Östergötland, Linköping, Sweden
| | - Kyoko Watanabe
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, the Netherlands
| | - Stefan Weiss
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Frank U Weiss
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Omer Weissbrod
- School of Public Health, Harvard University, Boston, MA, USA
| | - Harm-Jan Westra
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gonneke Willemsen
- Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Haydeh Payami
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Daisy M A E Jonkers
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, the Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Alejandro Arias Vasquez
- Department of Psychiatry, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Eco J C de Geus
- Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
- Amsterdam Public Health, Amsterdam UMC, Amsterdam, the Netherlands
| | - Katie A Meyer
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Jakob Stokholm
- COPSAC, Copenhagen University Hospital, Copenhagen, Denmark
| | - Eran Segal
- Department of Computer Science and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Elin Org
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hyung-Lae Kim
- Department of Biochemistry, Ewha Womans University School of Medicine, Seoul, Republic of Korea
| | - Robert C Kaplan
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Markus M Lerch
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Istituto di Ricerca Genetica e Biomedica, National Research Council, Monserrato, Italy
| | - Mauro D'Amato
- Center for Molecular Medicine and Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Department of Gastrointestinal and Liver Diseases, Biodonostia Health Research Institute, San Sebastián, Spain
- Ikerbasque, Basque Science Foundation, Bilbao, Spain
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrew D Paterson
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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Chen L, van den Munckhof ICL, Schraa K, Ter Horst R, Koehorst M, van Faassen M, van der Ley C, Doestzada M, Zhernakova DV, Kurilshikov A, Bloks VW, Groen AK, Riksen NP, Rutten JHW, Joosten LAB, Wijmenga C, Zhernakova A, Netea MG, Fu J, Kuipers F. Genetic and Microbial Associations to Plasma and Fecal Bile Acids in Obesity Relate to Plasma Lipids and Liver Fat Content. Cell Rep 2020; 33:108212. [PMID: 33027657 DOI: 10.1016/j.celrep.2020.108212] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/31/2020] [Accepted: 09/09/2020] [Indexed: 12/21/2022] Open
Abstract
Bile acids (BAs) are implicated in the etiology of obesity-related conditions such as non-alcoholic fatty liver disease. Differently structured BA species display variable signaling activities via farnesoid X receptor (FXR) and Takeda G protein-coupled BA receptor 1 (TGR5). This study profiles plasma and fecal BAs and plasma 7α-hydroxy-4-cholesten-3-one (C4) in 297 persons with obesity, identifies underlying genetic and microbial determinants, and establishes BA correlations with liver fat and plasma lipid parameters. We identify 27 genetic associations (p < 5 × 10-8) and 439 microbial correlations (FDR < 0.05) for 50 BA entities. Additionally, we report 111 correlations between BA and 88 lipid parameters (FDR < 0.05), mainly for C4 reflecting hepatic BA synthesis. Inter-individual variability in the plasma BA profile does not reflect hepatic BA synthetic pathways, but rather transport and metabolism within the enterohepatic circulation. Our study reveals genetic and microbial determinants of BAs in obesity and their relationship to disease-relevant lipid parameters that are important for the design of personalized therapies targeting BA-signaling pathways.
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Affiliation(s)
- Lianmin Chen
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Inge C L van den Munckhof
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6500HB, the Netherlands
| | - Kiki Schraa
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6500HB, the Netherlands
| | - Rob Ter Horst
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6500HB, the Netherlands
| | - Martijn Koehorst
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Martijn van Faassen
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Claude van der Ley
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Marwah Doestzada
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Daria V Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO University, St. Petersburg 197101, Russia
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Vincent W Bloks
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Albert K Groen
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Department of Vascular Medicine, University of Amsterdam, Amsterdam University Medical Center, Amsterdam 1012WX, the Netherlands
| | | | - Niels P Riksen
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6500HB, the Netherlands
| | - Joost H W Rutten
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6500HB, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6500HB, the Netherlands; Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca 400000, Romania
| | - Cisca Wijmenga
- University of Groningen, Groningen 9712CP, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6500HB, the Netherlands; Department for Genomics & Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn 53113, Germany; Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Craiova 200349, Romania
| | - Jingyuan Fu
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands.
| | - Folkert Kuipers
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands; Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen 9713AV, the Netherlands.
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30
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Chen L, Collij V, Jaeger M, van den Munckhof ICL, Vich Vila A, Kurilshikov A, Gacesa R, Sinha T, Oosting M, Joosten LAB, Rutten JHW, Riksen NP, Xavier RJ, Kuipers F, Wijmenga C, Zhernakova A, Netea MG, Weersma RK, Fu J. Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity. Nat Commun 2020; 11:4018. [PMID: 32782301 PMCID: PMC7419557 DOI: 10.1038/s41467-020-17840-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 07/20/2020] [Indexed: 02/07/2023] Open
Abstract
The gut microbiome is an ecosystem that involves complex interactions. Currently, our knowledge about the role of the gut microbiome in health and disease relies mainly on differential microbial abundance, and little is known about the role of microbial interactions in the context of human disease. Here, we construct and compare microbial co-abundance networks using 2,379 metagenomes from four human cohorts: an inflammatory bowel disease (IBD) cohort, an obese cohort and two population-based cohorts. We find that the strengths of 38.6% of species co-abundances and 64.3% of pathway co-abundances vary significantly between cohorts, with 113 species and 1,050 pathway co-abundances showing IBD-specific effects and 281 pathway co-abundances showing obesity-specific effects. We can also replicate these IBD microbial co-abundances in longitudinal data from the IBD cohort of the integrative human microbiome (iHMP-IBD) project. Our study identifies several key species and pathways in IBD and obesity and provides evidence that altered microbial abundances in disease can influence their co-abundance relationship, which expands our current knowledge regarding microbial dysbiosis in disease. Gut microbiome alterations have been linked to inflammatory bowel disease (IBD) and obesity. Here, the authors characterize the metagenomes of four large human cohorts and perform co-abundance network analysis showing that dysbiosis in disease is marked by the altered co-abundance relationships, suggesting that pathway coabundance networks are more heterogeneous than species network.
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Affiliation(s)
- Lianmin Chen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Valerie Collij
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Martin Jaeger
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Inge C L van den Munckhof
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marije Oosting
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Joost H W Rutten
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Niels P Riksen
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ramnik J Xavier
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Folkert Kuipers
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,University of Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.,Department for Genomics & Immunoregulation, Life and Medical Sciences Institute, University of Bonn, 53115, Bonn, Germany.,Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Craiova, Romania
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. .,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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31
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Ricaño-Ponce I, Gutierrez-Achury J, Costa AF, Deelen P, Kurilshikov A, Zorro MM, Platteel M, van der Graaf A, Sanna S, Daffra O, Zhernakova A, Fu J, Trynka G, Smecuol E, Niveloni SI, Bai JC, Kumar V, Wijmenga C. Immunochip meta-analysis in European and Argentinian populations identifies two novel genetic loci associated with celiac disease. Eur J Hum Genet 2020; 28:313-323. [PMID: 31591516 PMCID: PMC7028987 DOI: 10.1038/s41431-019-0520-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 09/03/2019] [Accepted: 09/10/2019] [Indexed: 12/30/2022] Open
Abstract
Celiac disease (CeD) is a common immune-mediated disease of the small intestine that is triggered by exposure to dietary gluten. While the HLA locus plays a major role in disease susceptibility, 39 non-HLA loci were also identified in a study of 24,269 individuals. We now build on this earlier study by adding 4125 additional Caucasian samples including an Argentinian cohort. In doing so, we not only confirm the previous associations, we also identify two novel independent genome-wide significant associations at loci: 12p13.31 and 22q13.1. By applying a genomics approach and differential expression analysis in CeD intestinal biopsies, we prioritize potential causal genes at these novel loci, including LTBR, CYTH4, and RAC2. Nineteen prioritized causal genes are overlapping known drug targets. Pathway enrichment analysis and expression of these genes in CeD biopsies suggest that they have roles in regulating multiple pathways such as the tumor necrosis factor (TNF) mediated signaling pathway and positive regulation of I-κB kinase/NF-κB signaling.
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Affiliation(s)
- Isis Ricaño-Ponce
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Javier Gutierrez-Achury
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Ana Florencia Costa
- Small Bowel Section, Department of Medicine, Dr. C. Bonorino Udaondo Gastroenterology Hospital, Buenos Aires, Argentina
| | - Patrick Deelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Maria Magdalena Zorro
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Mathieu Platteel
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Adriaan van der Graaf
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Serena Sanna
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Oscar Daffra
- Gastroenterology Service, OSEP Mendoza, Mendoza, Argentina
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
| | - Gosia Trynka
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Edgardo Smecuol
- Small Bowel Section, Department of Medicine, Dr. C. Bonorino Udaondo Gastroenterology Hospital, Buenos Aires, Argentina
| | - Sonia Isabel Niveloni
- Small Bowel Section, Department of Medicine, Dr. C. Bonorino Udaondo Gastroenterology Hospital, Buenos Aires, Argentina
| | - Julio Cesar Bai
- Small Bowel Section, Department of Medicine, Dr. C. Bonorino Udaondo Gastroenterology Hospital, Buenos Aires, Argentina
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525GA, Nijmegen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700RB, Groningen, the Netherlands.
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.
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32
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Aardema H, Lisotto P, Kurilshikov A, Diepeveen JRJ, Friedrich AW, Sinha B, de Smet AMGA, Harmsen HJM. Marked Changes in Gut Microbiota in Cardio-Surgical Intensive Care Patients: A Longitudinal Cohort Study. Front Cell Infect Microbiol 2020; 9:467. [PMID: 32010644 PMCID: PMC6974539 DOI: 10.3389/fcimb.2019.00467] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022] Open
Abstract
Background: Virtually no studies on the dynamics of the intestinal microbiota in patients admitted to the intensive care unit (ICU) are published, despite the increasingly recognized important role of microbiota on human physiology. Critical care patients undergo treatments that are known to influence the microbiota. However, dynamics and extent of such changes are not yet fully understood. To address this topic, we analyzed the microbiota before, during and after planned major cardio surgery that, for the first time, allowed us to follow the microbial dynamics of critical care patients. In this prospective, observational, longitudinal, single center study, we analyzed the fecal microbiota using 16S rRNA gene sequencing. Results: Samples of 97 patients admitted between April 2015 and November 2016 were included. In 32 patients, data of all three time points (before, during and after admission) were available for analysis. We found a large intra-individual variation in composition of gut microbiota. During admission, a significant change in microbial composition occurred in most patients, with a significant increase in pathobionts combined with a decrease in strictly anaerobic gut bacteria, typically beneficial for health. A lower bacterial diversity during admission was associated with longer hospitalization. In most patients analyzed at all three time points, the change in microbiota during hospital stay reverted to the original composition post-discharge. Conclusions: Our study shows that, even with a short ICU stay, patients present a significant change in microbial composition shortly after admission. The unique longitudinal setup of this study displayed a restoration of the microbiota in most patients to baseline composition post-discharge, which demonstrated its great restorative capacity. A relative decrease in benign or even beneficial bacteria and increase of pathobionts shifts the microbial balance in the gut, which could have clinical relevance. In future studies, the microbiota of ICU patients should be considered a good target for optimisation.
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Affiliation(s)
- Heleen Aardema
- Department of Critical Care, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Paola Lisotto
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Janneke R J Diepeveen
- Department of Critical Care, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alex W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Bhanu Sinha
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Anne Marie G A de Smet
- Department of Critical Care, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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33
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Vojinovic D, Radjabzadeh D, Kurilshikov A, Amin N, Wijmenga C, Franke L, Ikram MA, Uitterlinden AG, Zhernakova A, Fu J, Kraaij R, van Duijn CM. Relationship between gut microbiota and circulating metabolites in population-based cohorts. Nat Commun 2019; 10:5813. [PMID: 31862950 PMCID: PMC6925111 DOI: 10.1038/s41467-019-13721-1] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 11/13/2019] [Indexed: 12/29/2022] Open
Abstract
Gut microbiota has been implicated in major diseases affecting the human population and has also been linked to triglycerides and high-density lipoprotein levels in the circulation. Recent development in metabolomics allows classifying the lipoprotein particles into more details. Here, we examine the impact of gut microbiota on circulating metabolites measured by Nuclear Magnetic Resonance technology in 2309 individuals from the Rotterdam Study and the LifeLines-DEEP cohort. We assess the relationship between gut microbiota and metabolites by linear regression analysis while adjusting for age, sex, body-mass index, technical covariates, medication use, and multiple testing. We report an association of 32 microbial families and genera with very-low-density and high-density subfractions, serum lipid measures, glycolysis-related metabolites, ketone bodies, amino acids, and acute-phase reaction markers. These observations provide insights into the role of microbiota in host metabolism and support the potential of gut microbiota as a target for therapeutic and preventive interventions.
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Affiliation(s)
- Dina Vojinovic
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Alexander Kurilshikov
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
- Nuffield Department of Population Health, University of Oxford, Oxford, UK.
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34
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Garmaeva S, Sinha T, Kurilshikov A, Fu J, Wijmenga C, Zhernakova A. Studying the gut virome in the metagenomic era: challenges and perspectives. BMC Biol 2019; 17:84. [PMID: 31660953 PMCID: PMC6819614 DOI: 10.1186/s12915-019-0704-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 12/12/2022] Open
Abstract
The human gut harbors a complex ecosystem of microorganisms, including bacteria and viruses. With the rise of next-generation sequencing technologies, we have seen a quantum leap in the study of human-gut-inhabiting bacteria, yet the viruses that infect these bacteria, known as bacteriophages, remain underexplored. In this review, we focus on what is known about the role of bacteriophages in human health and the technical challenges involved in studying the gut virome, of which they are a major component. Lastly, we discuss what can be learned from studies of bacteriophages in other ecosystems.
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Affiliation(s)
- Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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35
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Vich Vila A, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF, Dekens J, Peters V, Voskuil MD, Visschedijk MC, van Dullemen HM, Keszthelyi D, Swertz MA, Franke L, Alberts R, Festen EAM, Dijkstra G, Masclee AAM, Hofker MH, Xavier RJ, Alm EJ, Fu J, Wijmenga C, Jonkers DMAE, Zhernakova A, Weersma RK. Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome. Sci Transl Med 2019; 10:10/472/eaap8914. [PMID: 30567928 DOI: 10.1126/scitranslmed.aap8914] [Citation(s) in RCA: 285] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 04/06/2018] [Accepted: 07/16/2018] [Indexed: 12/15/2022]
Abstract
Changes in the gut microbiota have been associated with two of the most common gastrointestinal diseases, inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). Here, we performed a case-control analysis using shotgun metagenomic sequencing of stool samples from 1792 individuals with IBD and IBS compared with control individuals in the general population. Despite substantial overlap between the gut microbiome of patients with IBD and IBS compared with control individuals, we were able to use gut microbiota composition differences to distinguish patients with IBD from those with IBS. By combining species-level profiles and strain-level profiles with bacterial growth rates, metabolic functions, antibiotic resistance, and virulence factor analyses, we identified key bacterial species that may be involved in two common gastrointestinal diseases.
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Affiliation(s)
- Arnau Vich Vila
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Floris Imhann
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Valerie Collij
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Soesma A Jankipersadsing
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Thomas Gurry
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Zlatan Mujagic
- Maastricht University Medical Center+, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, Netherlands
| | - Alexander Kurilshikov
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Marc Jan Bonder
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Xiaofang Jiang
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ettje F Tigchelaar
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Jackie Dekens
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Vera Peters
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands
| | - Michiel D Voskuil
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Marijn C Visschedijk
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Hendrik M van Dullemen
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands
| | - Daniel Keszthelyi
- Maastricht University Medical Center+, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, Netherlands
| | - Morris A Swertz
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Lude Franke
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Rudi Alberts
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Eleonora A M Festen
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Gerard Dijkstra
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands
| | - Ad A M Masclee
- Maastricht University Medical Center+, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, Netherlands
| | - Marten H Hofker
- University of Groningen and University Medical Center Groningen, Department of Pediatrics, Groningen, Netherlands
| | - Ramnik J Xavier
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Eric J Alm
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jingyuan Fu
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands.,University of Groningen and University Medical Center Groningen, Department of Pediatrics, Groningen, Netherlands
| | - Cisca Wijmenga
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Daisy M A E Jonkers
- Maastricht University Medical Center+, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, Netherlands
| | - Alexandra Zhernakova
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
| | - Rinse K Weersma
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, Netherlands.
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36
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Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019. [PMID: 31285584 DOI: 10.1038/s41564-019-04904-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
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37
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Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019; 4:1727-1736. [PMID: 31285584 DOI: 10.1101/527796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 05/22/2019] [Indexed: 05/26/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
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Kurilshikov A, van den Munckhof ICL, Chen L, Bonder MJ, Schraa K, Rutten JHW, Riksen NP, de Graaf J, Oosting M, Sanna S, Joosten LAB, van der Graaf M, Brand T, Koonen DPY, van Faassen M, Slagboom PE, Xavier RJ, Kuipers F, Hofker MH, Wijmenga C, Netea MG, Zhernakova A, Fu J. Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk. Circ Res 2019; 124:1808-1820. [PMID: 30971183 DOI: 10.1161/circresaha.118.314642] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RATIONALE Altered gut microbial composition has been linked to cardiovascular diseases (CVDs), but its functional links to host metabolism and immunity in relation to CVD development remain unclear. OBJECTIVES To systematically assess functional links between the microbiome and the plasma metabolome, cardiometabolic phenotypes, and CVD risk and to identify diet-microbe-metabolism-immune interactions in well-documented cohorts. METHODS AND RESULTS We assessed metagenomics-based microbial associations between 231 plasma metabolites and microbial species and pathways in the population-based LLD (Lifelines DEEP) cohort (n=978) and a clinical obesity cohort (n=297). After correcting for age, sex, and body mass index, the gut microbiome could explain ≤11.1% and 16.4% of the variation in plasma metabolites in the population-based and obesity cohorts, respectively. Obese-specific microbial associations were found for lipid compositions in the VLDL, IDL, and LDL lipoprotein subclasses. Bacterial L-methionine biosynthesis and a Ruminococcus species were associated to cardiovascular phenotypes in obese individuals, namely atherosclerosis and liver fat content, respectively. Integration of microbiome-diet-inflammation analysis in relation to metabolic risk score of CVD in the population cohort revealed 48 microbial pathways associated to CVD risk that were largely independent of diet and inflammation. Our data also showed that plasma levels rather than fecal levels of short-chain fatty acids were relevant to inflammation and CVD risk. CONCLUSIONS This study presents the largest metagenome-based association study on plasma metabolism and microbiome relevance to diet, inflammation, CVD risk, and cardiometabolic phenotypes in both population-based and clinical obesity cohorts. Our findings identified novel bacterial species and pathways that associated to specific lipoprotein subclasses and revealed functional links between the gut microbiome and host health that provide a basis for developing microbiome-targeted therapy for disease prevention and treatment.
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Affiliation(s)
- Alexander Kurilshikov
- From the Department of Genetics (A.K., L.C., M.J.B., S.S., C.W., A.Z., J.F.), University of Groningen, University Medical Center Groningen, the Netherlands
| | - Inge C L van den Munckhof
- Department of Internal Medicine and Radboud Center for Infectious Diseases (I.C.L.v.d.M., K.S., J.H.W.R., N.P.R., J.d.G., M.O., L.A.B.J., T.B., M.G.N.), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lianmin Chen
- From the Department of Genetics (A.K., L.C., M.J.B., S.S., C.W., A.Z., J.F.), University of Groningen, University Medical Center Groningen, the Netherlands.,Department of Pediatrics (L.C., D.P.Y.K., F.K., M.H.H., J.F.), University of Groningen, University Medical Center Groningen, the Netherlands
| | - Marc J Bonder
- From the Department of Genetics (A.K., L.C., M.J.B., S.S., C.W., A.Z., J.F.), University of Groningen, University Medical Center Groningen, the Netherlands
| | - Kiki Schraa
- Department of Internal Medicine and Radboud Center for Infectious Diseases (I.C.L.v.d.M., K.S., J.H.W.R., N.P.R., J.d.G., M.O., L.A.B.J., T.B., M.G.N.), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Joost H W Rutten
- Department of Internal Medicine and Radboud Center for Infectious Diseases (I.C.L.v.d.M., K.S., J.H.W.R., N.P.R., J.d.G., M.O., L.A.B.J., T.B., M.G.N.), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Niels P Riksen
- Department of Internal Medicine and Radboud Center for Infectious Diseases (I.C.L.v.d.M., K.S., J.H.W.R., N.P.R., J.d.G., M.O., L.A.B.J., T.B., M.G.N.), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jacqueline de Graaf
- Department of Internal Medicine and Radboud Center for Infectious Diseases (I.C.L.v.d.M., K.S., J.H.W.R., N.P.R., J.d.G., M.O., L.A.B.J., T.B., M.G.N.), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marije Oosting
- Department of Internal Medicine and Radboud Center for Infectious Diseases (I.C.L.v.d.M., K.S., J.H.W.R., N.P.R., J.d.G., M.O., L.A.B.J., T.B., M.G.N.), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Serena Sanna
- From the Department of Genetics (A.K., L.C., M.J.B., S.S., C.W., A.Z., J.F.), University of Groningen, University Medical Center Groningen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases (I.C.L.v.d.M., K.S., J.H.W.R., N.P.R., J.d.G., M.O., L.A.B.J., T.B., M.G.N.), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marinette van der Graaf
- Department of Radiology and Nuclear Medicine (M.v.d.G.), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tessa Brand
- Department of Internal Medicine and Radboud Center for Infectious Diseases (I.C.L.v.d.M., K.S., J.H.W.R., N.P.R., J.d.G., M.O., L.A.B.J., T.B., M.G.N.), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Debby P Y Koonen
- Department of Pediatrics (L.C., D.P.Y.K., F.K., M.H.H., J.F.), University of Groningen, University Medical Center Groningen, the Netherlands
| | - Martijn van Faassen
- Department of Laboratory Medicine (M.v.F., F.K.), University of Groningen, University Medical Center Groningen, the Netherlands
| | | | - P Eline Slagboom
- Section of Molecular Epidemiology, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, the Netherlands (P.E.S.)
| | - Ramnik J Xavier
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston (R.J.X.).,Broad Institute of MIT and Harvard, Cambridge, MA (R.J.X.).,Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston (R.J.X.).,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge (R.J.X.)
| | - Folkert Kuipers
- Department of Pediatrics (L.C., D.P.Y.K., F.K., M.H.H., J.F.), University of Groningen, University Medical Center Groningen, the Netherlands.,Department of Laboratory Medicine (M.v.F., F.K.), University of Groningen, University Medical Center Groningen, the Netherlands
| | - Marten H Hofker
- Department of Pediatrics (L.C., D.P.Y.K., F.K., M.H.H., J.F.), University of Groningen, University Medical Center Groningen, the Netherlands
| | - Cisca Wijmenga
- From the Department of Genetics (A.K., L.C., M.J.B., S.S., C.W., A.Z., J.F.), University of Groningen, University Medical Center Groningen, the Netherlands.,Department of Immunology, K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Norway (C.W.)
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (I.C.L.v.d.M., K.S., J.H.W.R., N.P.R., J.d.G., M.O., L.A.B.J., T.B., M.G.N.), Radboud University Medical Center, Nijmegen, the Netherlands.,Department for Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Germany (M.G.N.).,Human Genomics Laboratory, Craiova University of Medicine and Pharmacy, Romania (M.G.N.)
| | - Alexandra Zhernakova
- From the Department of Genetics (A.K., L.C., M.J.B., S.S., C.W., A.Z., J.F.), University of Groningen, University Medical Center Groningen, the Netherlands
| | - Jingyuan Fu
- From the Department of Genetics (A.K., L.C., M.J.B., S.S., C.W., A.Z., J.F.), University of Groningen, University Medical Center Groningen, the Netherlands.,Department of Pediatrics (L.C., D.P.Y.K., F.K., M.H.H., J.F.), University of Groningen, University Medical Center Groningen, the Netherlands
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39
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Sanna S, van Zuydam NR, Mahajan A, Kurilshikov A, Vich Vila A, Võsa U, Mujagic Z, Masclee AAM, Jonkers DMAE, Oosting M, Joosten LAB, Netea MG, Franke L, Zhernakova A, Fu J, Wijmenga C, McCarthy MI. Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases. Nat Genet 2019; 51:600-605. [PMID: 30778224 PMCID: PMC6441384 DOI: 10.1038/s41588-019-0350-x] [Citation(s) in RCA: 697] [Impact Index Per Article: 139.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 01/10/2019] [Indexed: 12/18/2022]
Abstract
Microbiome-wide association studies on large population cohorts have highlighted associations between the gut microbiome and complex traits, including type 2 diabetes (T2D) and obesity1. However, the causal relationships remain largely unresolved. We leveraged information from 952 normoglycemic individuals for whom genome-wide genotyping, gut metagenomic sequence and fecal short-chain fatty acid (SCFA) levels were available2, then combined this information with genome-wide-association summary statistics for 17 metabolic and anthropometric traits. Using bidirectional Mendelian randomization (MR) analyses to assess causality3, we found that the host-genetic-driven increase in gut production of the SCFA butyrate was associated with improved insulin response after an oral glucose-tolerance test (P = 9.8 × 10-5), whereas abnormalities in the production or absorption of another SCFA, propionate, were causally related to an increased risk of T2D (P = 0.004). These data provide evidence of a causal effect of the gut microbiome on metabolic traits and support the use of MR as a means to elucidate causal relationships from microbiome-wide association findings.
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Affiliation(s)
- Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | - Natalie R van Zuydam
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes Endocrinology and Metabolism, Churchill Hospital, University of Oxford, Oxford, UK
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes Endocrinology and Metabolism, Churchill Hospital, University of Oxford, Oxford, UK
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Urmo Võsa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Zlatan Mujagic
- Maastricht University Medical Center, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, the Netherlands
| | - Ad A M Masclee
- Maastricht University Medical Center, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, the Netherlands
| | - Daisy M A E Jonkers
- Maastricht University Medical Center, Division Gastroenterology-Hepatology, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht, the Netherlands
| | - Marije Oosting
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS) and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, Groningen, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Oxford Centre for Diabetes Endocrinology and Metabolism, Churchill Hospital, University of Oxford, Oxford, UK.
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.
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Zeevi D, Korem T, Godneva A, Bar N, Kurilshikov A, Lotan-Pompan M, Weinberger A, Fu J, Wijmenga C, Zhernakova A, Segal E. Structural variation in the gut microbiome associates with host health. Nature 2019; 568:43-48. [PMID: 30918406 DOI: 10.1038/s41586-019-1065-y] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 02/21/2019] [Indexed: 12/16/2022]
Abstract
Differences in the presence of even a few genes between otherwise identical bacterial strains may result in critical phenotypic differences. Here we systematically identify microbial genomic structural variants (SVs) and find them to be prevalent in the human gut microbiome across phyla and to replicate in different cohorts. SVs are enriched for CRISPR-associated and antibiotic-producing functions and depleted from housekeeping genes, suggesting that they have a role in microbial adaptation. We find multiple associations between SVs and host disease risk factors, many of which replicate in an independent cohort. Exploring genes that are clustered in the same SV, we uncover several possible mechanistic links between the microbiome and its host, including a region in Anaerostipes hadrus that encodes a composite inositol catabolism-butyrate biosynthesis pathway, the presence of which is associated with lower host metabolic disease risk. Overall, our results uncover a nascent layer of variability in the microbiome that is associated with microbial adaptation and host health.
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Affiliation(s)
- David Zeevi
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel. .,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. .,Center for Studies in Physics and Biology, The Rockefeller University, New York, NY, USA.
| | - Tal Korem
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.,Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Anastasia Godneva
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Bar
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Kurilshikov
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Maya Lotan-Pompan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,Department of Immunology, K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel. .,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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41
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Valles-Colomer M, Falony G, Darzi Y, Tigchelaar EF, Wang J, Tito RY, Schiweck C, Kurilshikov A, Joossens M, Wijmenga C, Claes S, Van Oudenhove L, Zhernakova A, Vieira-Silva S, Raes J. The neuroactive potential of the human gut microbiota in quality of life and depression. Nat Microbiol 2019; 4:623-632. [DOI: 10.1038/s41564-018-0337-x] [Citation(s) in RCA: 784] [Impact Index Per Article: 156.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 12/05/2018] [Indexed: 11/09/2022]
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42
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van der Meulen TA, Harmsen HJ, Vila AV, Kurilshikov A, Liefers SC, Zhernakova A, Fu J, Wijmenga C, Weersma RK, de Leeuw K, Bootsma H, Spijkervet FK, Vissink A, Kroese FG. Shared gut, but distinct oral microbiota composition in primary Sjögren's syndrome and systemic lupus erythematosus. J Autoimmun 2019; 97:77-87. [DOI: 10.1016/j.jaut.2018.10.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/12/2018] [Accepted: 10/16/2018] [Indexed: 12/11/2022]
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43
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van den Munckhof ICL, Kurilshikov A, Ter Horst R, Riksen NP, Joosten LAB, Zhernakova A, Fu J, Keating ST, Netea MG, de Graaf J, Rutten JHW. Role of gut microbiota in chronic low-grade inflammation as potential driver for atherosclerotic cardiovascular disease: a systematic review of human studies. Obes Rev 2018; 19:1719-1734. [PMID: 30144260 DOI: 10.1111/obr.12750] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 12/11/2022]
Abstract
A hallmark of obesity is chronic low-grade inflammation, which plays a major role in the process of atherosclerotic cardiovascular disease (ACVD). Gut microbiota is one of the factors influencing systemic immune responses, and profound changes have been found in its composition and metabolic function in individuals with obesity. This systematic review assesses the association between the gut microbiota and markers of low-grade inflammation in humans. We identified 14 studies which were mostly observational and relatively small (n = 10 to 471). The way in which the microbiome is analysed differed extensively between these studies. Lower gut microbial diversity was associated with higher white blood cell counts and high sensitivity C-reactive protein (hsCRP) levels. The abundance of Bifidobacterium, Faecalibacterium, Ruminococcus and Prevotella were inversely related to different markers of low-grade inflammation such as hsCRP and interleukin (IL)-6. In addition, this review speculates on possible mechanisms through which the gut microbiota can affect low-grade inflammation and thereby ACVD. We discuss the associations between the microbiome and the inflammasome, the innate immune system, bile acids, gut permeability, the endocannabinoid system and TMAO. These data reinforce the importance of human research into the gut microbiota as potential diagnostic and therapeutic strategy to prevent ACVD.
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Affiliation(s)
- I C L van den Munckhof
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - A Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - R Ter Horst
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N P Riksen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - L A B Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - A Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - J Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - S T Keating
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Department for Genomics and Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - J de Graaf
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - J H W Rutten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
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44
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Sinha T, Vich Vila A, Garmaeva S, Jankipersadsing SA, Imhann F, Collij V, Bonder MJ, Jiang X, Gurry T, Alm EJ, D’Amato M, Weersma RK, Scherjon S, Wijmenga C, Fu J, Kurilshikov A, Zhernakova A. Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles. Gut Microbes 2018; 10:358-366. [PMID: 30373468 PMCID: PMC6546312 DOI: 10.1080/19490976.2018.1528822] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Several gastrointestinal diseases show a sex imbalance, although the underlying (patho)physiological mechanisms behind this are not well understood. The gut microbiome may be involved in this process, forming a complex interaction with host immune system, sex hormones, medication and other environmental factors. Here we performed sex-specific analyses of fecal microbiota composition in 1135 individuals from a population-based cohort. The overall gut microbiome composition of females and males was significantly different (p = 0.001), with females showing a greater microbial diversity (p = 0.009). After correcting for the effects of intrinsic factors, smoking, diet and medications, female hormonal factors such as the use of oral contraceptives and undergoing an ovariectomy were associated with microbial species and pathways. Females had a higher richness of antibiotic-resistance genes, with the most notable being resistance to the lincosamide nucleotidyltransferase (LNU) gene family. The higher abundance of resistance genes is consistent with the greater prescription of the Macrolide-Lincosamide-Streptogramin classes of antibiotics to females. Furthermore, we observed an increased resistance to aminoglycosides in females with self-reported irritable bowel syndrome. These results throw light upon the effects of common medications that are differentially prescribed between sexes and highlight the importance of sex-specific analysis when studying the gut microbiome and resistome.
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Affiliation(s)
- Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sanzhima Garmaeva
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Soesma A. Jankipersadsing
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Floris Imhann
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Valerie Collij
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Xiaofang Jiang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas Gurry
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eric J. Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mauro D’Amato
- Gastrointestinal Genetics Unit, Biodonostia Health Research Institute, San Sebastian, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sicco Scherjon
- Department of Obstetrics and Gynecology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Department of Immunology, K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands,CONTACT Alexandra Zhernakova, Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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45
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Zhernakova DV, Le TH, Kurilshikov A, Atanasovska B, Bonder MJ, Sanna S, Claringbould A, Võsa U, Deelen P, Franke L, de Boer RA, Kuipers F, Netea MG, Hofker MH, Wijmenga C, Zhernakova A, Fu J. Author Correction: Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome. Nat Genet 2018; 50:1752. [PMID: 30341443 DOI: 10.1038/s41588-018-0275-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this paper originally published, there was a typographical error. In the Discussion, the sentence "In line with this, Ep-CAM-deficient mice exhibited increased intestinal permeability and decreased ion transport60, which may contribute to CVD susceptibility risk59" originally read iron instead of ion transport. This error has been corrected in the HTML, PDF and print versions of the article.
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Affiliation(s)
- Daria V Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russian Federation
| | - Trang H Le
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Biljana Atanasovska
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marc Jan Bonder
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Serena Sanna
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Annique Claringbould
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Urmo Võsa
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Patrick Deelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Rudolf A de Boer
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Folkert Kuipers
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.,Department for Genomics and Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Marten H Hofker
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | - Jingyuan Fu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands. .,Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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46
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Wang J, Kurilshikov A, Radjabzadeh D, Turpin W, Croitoru K, Bonder MJ, Jackson MA, Medina-Gomez C, Frost F, Homuth G, Rühlemann M, Hughes D, Kim HN, Spector TD, Bell JT, Steves CJ, Timpson N, Franke A, Wijmenga C, Meyer K, Kacprowski T, Franke L, Paterson AD, Raes J, Kraaij R, Zhernakova A. Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative. Microbiome 2018; 6:101. [PMID: 29880062 PMCID: PMC5992867 DOI: 10.1186/s40168-018-0479-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/10/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND In recent years, human microbiota, especially gut microbiota, have emerged as an important yet complex trait influencing human metabolism, immunology, and diseases. Many studies are investigating the forces underlying the observed variation, including the human genetic variants that shape human microbiota. Several preliminary genome-wide association studies (GWAS) have been completed, but more are necessary to achieve a fuller picture. RESULTS Here, we announce the MiBioGen consortium initiative, which has assembled 18 population-level cohorts and some 19,000 participants. Its aim is to generate new knowledge for the rapidly developing field of microbiota research. Each cohort has surveyed the gut microbiome via 16S rRNA sequencing and genotyped their participants with full-genome SNP arrays. We have standardized the analytical pipelines for both the microbiota phenotypes and genotypes, and all the data have been processed using identical approaches. Our analysis of microbiome composition shows that we can reduce the potential artifacts introduced by technical differences in generating microbiota data. We are now in the process of benchmarking the association tests and performing meta-analyses of genome-wide associations. All pipeline and summary statistics results will be shared using public data repositories. CONCLUSION We present the largest consortium to date devoted to microbiota-GWAS. We have adapted our analytical pipelines to suit multi-cohort analyses and expect to gain insight into host-microbiota cross-talk at the genome-wide level. And, as an open consortium, we invite more cohorts to join us (by contacting one of the corresponding authors) and to follow the analytical pipeline we have developed.
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Affiliation(s)
- Jun Wang
- CAS Key Laboratory for Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Department of Microbiology and Immunology, Rega Institute. KU Leuven - University of Leuven, Leuven, Belgium.
- VIB Center for Microbiology, Leuven, Belgium.
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Williams Turpin
- Division of Gastroenterology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Kenneth Croitoru
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Matthew A Jackson
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, 3000, CA, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, 3000, CA, Rotterdam, The Netherlands
| | - Fabian Frost
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Malte Rühlemann
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - David Hughes
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Han-Na Kim
- Department of Biochemistry, School of Medicine, Ewha Womans University, Seoul, South Korea
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Nicolas Timpson
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Katie Meyer
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Tim Kacprowski
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Andrew D Paterson
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute. KU Leuven - University of Leuven, Leuven, Belgium.
- VIB Center for Microbiology, Leuven, Belgium.
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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47
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van den Munckhof IC, Kurilshikov A, Bonder MJ, Schraa K, Rutten JH, Riksen NP, de Graaf J, Oosting M, Joosten LA, Koonen D, Slagboom EP, Xavier RJ, Kuipers F, Hofker MH, Wijmenga C, Netea MG, Zhernakova A, Fu J. Microbial Impact on Plasma Metabolites is Linked to the Cardiovascular Risk and Phenotypes. ATHEROSCLEROSIS SUPP 2018. [DOI: 10.1016/j.atherosclerosissup.2018.04.366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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48
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Jackson MA, Bonder MJ, Kuncheva Z, Zierer J, Fu J, Kurilshikov A, Wijmenga C, Zhernakova A, Bell JT, Spector TD, Steves CJ. Detection of stable community structures within gut microbiota co-occurrence networks from different human populations. PeerJ 2018; 6:e4303. [PMID: 29441232 PMCID: PMC5807925 DOI: 10.7717/peerj.4303] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/10/2018] [Indexed: 12/20/2022] Open
Abstract
Microbes in the gut microbiome form sub-communities based on shared niche specialisations and specific interactions between individual taxa. The inter-microbial relationships that define these communities can be inferred from the co-occurrence of taxa across multiple samples. Here, we present an approach to identify comparable communities within different gut microbiota co-occurrence networks, and demonstrate its use by comparing the gut microbiota community structures of three geographically diverse populations. We combine gut microbiota profiles from 2,764 British, 1,023 Dutch, and 639 Israeli individuals, derive co-occurrence networks between their operational taxonomic units, and detect comparable communities within them. Comparing populations we find that community structure is significantly more similar between datasets than expected by chance. Mapping communities across the datasets, we also show that communities can have similar associations to host phenotypes in different populations. This study shows that the community structure within the gut microbiota is stable across populations, and describes a novel approach that facilitates comparative community-centric microbiome analyses.
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Affiliation(s)
- Matthew A Jackson
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Marc Jan Bonder
- University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, Netherlands
| | - Zhana Kuncheva
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Jonas Zierer
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom.,Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jingyuan Fu
- University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, Netherlands.,University Medical Center Groningen, Department of Pediatrics, University of Groningen, Groningen, Netherlands
| | - Alexander Kurilshikov
- University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, Netherlands
| | - Cisca Wijmenga
- University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, Netherlands.,K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway
| | - Alexandra Zhernakova
- University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, Netherlands
| | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Claire J Steves
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
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49
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Mironova N, Patutina O, Brenner E, Kurilshikov A, Vlassov V, Zenkova M. The systemic tumor response to RNase A treatment affects the expression of genes involved in maintaining cell malignancy. Oncotarget 2017; 8:78796-78810. [PMID: 29108266 PMCID: PMC5667999 DOI: 10.18632/oncotarget.20228] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/25/2017] [Indexed: 12/27/2022] Open
Abstract
Recently, pancreatic RNase A was shown to inhibit tumor and metastasis growth that accompanied by global alteration of miRNA profiles in the blood and tumor tissue (Mironova et al., 2013). Here, we performed a whole transcriptome analysis of murine Lewis lung carcinoma (LLC) after treatment of tumor-bearing mice with RNase A. We identified 966 differentially expressed transcripts in LLC tumors, of which 322 were upregulated and 644 were downregulated after RNase A treatment. Many of these genes are involved in signaling pathways that regulate energy metabolism, cell-growth promoting and transforming activity, modulation of the cancer microenvironment and extracellular matrix components, and cellular proliferation and differentiation. Following RNase A treatment, we detected an upregulation of carbohydrate metabolism, inositol phosphate cascade and oxidative phosphorylation, re-arrangement of cell adhesion, cell cycle control, apoptosis, and transcription. Whereas cancer-related signaling pathways (e.g., TGF-beta, JAK/STAT, and Wnt) were downregulated following RNase A treatment, as in the case of the PI3K/AKT pathway, which is involved in the progression of non-small lung cancer. RNase A therapy resulted in the downregulation of genes that inhibit the biogenesis of some miRNAs, particularly the let-7 miRNA family. Taken together, our data suggest that the antitumor activity and decreased invasion potential of tumor cells caused by RNase A are associated with enhanced energy cascade functioning, rearrangement of cancer-related events regulating cell growth and dissemination, and attenuation of signaling pathways having tumor-promoting activity. Thus, RNase A can be proposed as a potential component of anticancer therapy with multiple modes of action.
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Affiliation(s)
- Nadezhda Mironova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Olga Patutina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Evgenyi Brenner
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Alexander Kurilshikov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.,Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Marina Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
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50
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Shakhtshneider E, Ovsyannikova A, Ivanoshchuk D, Rymar O, Ragino Y, Kurilshikov A, Voevoda M. The spectrum of mutations in the CEL gene in early onset diabetes patients. Atherosclerosis 2017. [DOI: 10.1016/j.atherosclerosis.2017.06.841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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