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Genetics of human gut microbiome composition

Genetics of human gut microbiome composition

来源:bioRxiv_logobioRxiv
英文摘要

Abstract To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed whole-genome genotypes and 16S fecal microbiome data from 18,473 individuals (25 cohorts). Microbial composition showed high variability across cohorts: we detected only 9 out of 410 genera in more than 95% of the samples. A genome-wide association study (GWAS) of host genetic variation in relation to microbial taxa identified 30 loci affecting microbome taxa at a genome-wide significant (P<5×10-8) threshold. Just one locus, the lactase (LCT) gene region, reached study-wide significance (GWAS signal P=8.6×10?21); it showed an age-dependent association with Bifidobacterium abundance. Other associations were suggestive (1.94×10?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 analyses identified enrichment of microbiome trait loci SNPs in the metabolic, nutrition and environment domains and indicated food preferences and diseases as mediators of genetic effects.

J?rgensen Torben、van der Graaf Adriaan、Demirkan Ayse、Lieb Wolfgang、Kraaij Robert、Raes Jeroen、Stokholm Jakob、Org Elin、Spector Tim D.、Uitterlinden Andre G.、Franke Andre、Zhernakova Alexandra、Kim Han-Na、Barkan Elad、Shah Shiraz A.、Kurilshikov Alexander、Medina-Gomez Carolina、Bacigalupe Rodrigo、Wang Jun、Liu Xingrong、Hansen Tue H.、Frost Fabian、Turpin Williams、Vieira-Silva Sara、V?sa Urmo、Walter Susanna、Watanabe Kyoko、Weiss Stefan、Weiss Frank U.、Willemsen Gonneke、Jonkers Daisy M.A.E.、Vasquez Alejandro Arias、Jackson Matthew A.、Mujagic Zlatan、Qibin Qi、Rothschild Daphna、Shin Hocheol、Steves Claire J.、D?ˉAmato Mauro、Duijts Liesbeth、Burk Robert D.、Claringbould Annique、Fornage Myriam、Moll Henriette A.、Launer Lenore J.、Kim Hyung-Lae、Westra Harm-Jan、Wijmenga Cisca、Rivadeneira Fernando、Thorsen Jonathan、Hansen Torben、Finnicum Casey T.、Tito Raul Y.、V?lzke Henry、Paterson Andrew D.、Croitoru Kenneth、Wade Kaitlin H.、Radjabzadeh Djawad、Weissbrod Omer、S?rensen S?ren J.、Le Roy Caroline I.、R¨1hlemann Malte C.、Szopinska-Tokov Joanna、Hughes David A.、Timpson Nicholas J.、Zhernakova Daria V.、Kaplan Robert C.、Franke Lude、van Duijn Cornelia M.、Segal Eran、Borisevich Dmitrii、Laudes Matthias、Meyer Katie A.、Keszthelyi Daniel、Bisgaard Hans、Homuth Georg、Joossens Marie、de Geus Eco J.C.、Davies Gareth E.、Agreus Lars、Lusis Aldons J.、Lerch Markus M.、Andreasson Anna、Laakso Markku、Bedrani Larbi、Bonder Marc Jan、Sanna Serena、Payami Haydeh、L¨1ll Kreete、Knight Rob、V?lker Uwe、Falony Gwen、Raygoza Garay Juan Antonio、Moon Jee-Young、Bang Corinna、Bell Jordana T.、Jaddoe Vincent W.V.、Ijzerman Richard G.、Wallen Zachary D.、Boehnke Michael、Fu Jingyuan、Masclee Ad A.M.、Pedersen Oluf、Boomsma Dorret I.

Centre for Clinical Research and Disease Prevention, Bispebjerg/Frederiksberg Hospital, Capital Region of Copenhagen and Faculty of Health and Medical Sciences, University of CopenhagenDepartment of Genetics, University of Groningen, University Medical Center GroningenDepartment of Genetics, University of Groningen, University Medical Center Groningen||Section of Statistical Multi-Omics, Department of Clinical & Experimental Medicine, School of Biosciences & Medicine, University of SurreyInstitute of Epidemiology, Kiel UniversityDepartment of Internal Medicine, Erasmus MC University Medical CenterDepartment of Microbiology and Immunology, Rega Instituut||Center for MicrobiologyCOPSAC, Copenhagen University Hospital, Herlev-GentofteEstonian Genome Centre, Institute of Genomics, University of TartuDepartment of Twin Research & Genetic EpidemiologyDepartment of Internal Medicine, Erasmus MC University Medical Center||The Generation R Study, Erasmus MC University Medical Center||Department of Epidemiology, Erasmus MC University Medical CenterInstitute of Clinical Molecular Biology, Kiel UniversityDepartment of Genetics, University of Groningen, University Medical Center GroningenMedical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine||Department of Clinical Research Design and Evaluation, SAIHST, Sungkyunkwan UniversityDepartment of Computer Science and Cell Biology, Weizmann Institute of ScienceCOPSAC, Copenhagen University Hospital, Herlev-GentofteDepartment of Genetics, University of Groningen, University Medical Center GroningenDepartment of Internal Medicine, Erasmus MC University Medical Center||The Generation R Study, Erasmus MC University Medical CenterDepartment of Microbiology and Immunology, Rega Instituut||Center for MicrobiologyDepartment of Microbiology and Immunology, Rega Instituut||Center for Microbiology||Institute of Microbiology, Chinese Academy of SciencesCenter for Molecular Medicine and Unit of Clinical Epidemiology, Department of Medicine Solna, Karolinska InstitutetNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of CopenhagenDepartment of Medicine A, University Medicine GreifswaldDepartment of Medicine, University of Toronto||Division of Gastroenterology, Mount Sinai HospitalDepartment of Microbiology and Immunology, Rega Instituut||Center for MicrobiologyDepartment of Genetics, University of Groningen, University Medical Center GroningenDepartment of Biomedical and Clinical Sciences, University of Link?ping||Department of gastroenterology, County Council of ?sterg?tlandDepartment of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University AmsterdamDepartment of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine GreifswaldDepartment of Medicine A, University Medicine GreifswaldBiological Psychology, Vrije UniversiteitDivision of Gastroenterology-Hepatology, Maastricht University Medical Center+||NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht UniversityDepartment of Psychiatry, Radboudumc, Donders Institute for Brain, Cognition and Behaviour||Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and BehaviourSection of Statistical Multi-Omics, Department of Clinical & Experimental Medicine, School of Biosciences & Medicine, University of Surrey||Kennedy Institute of Rheumatology, University of OxfordDivision of Gastroenterology-Hepatology, Maastricht University Medical Center+||NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht UniversityDepartment of Epidemiology and Population Health, Albert Einstein College of MedicineDepartment of Computer Science and Cell Biology, Weizmann Institute of ScienceDepartment of Family Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine||Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of MedicineDepartment of Twin Research & Genetic EpidemiologyCenter for Molecular Medicine and Unit of Clinical Epidemiology, Department of Medicine Solna, Karolinska Institutet||School of Biological Sciences, Monash University||Department of Gastrointestinal and Liver Diseases, Biodonostia Health Research Institute||Ikerbasque, Basque Science FoundationThe Generation R Study, Erasmus MC University Medical Center||Department of Pediatrics, Erasmus MC University Medical CenterInstitute of Clinical Molecular Biology, Kiel University||Department of Pediatrics, Albert Einstein College of Medicine||Department of Microbiology & Immunology, Albert Einstein College of MedicineDepartment of Genetics, University of Groningen, University Medical Center GroningenInstitute of Molecular Medicine McGovern Medical School, The University of Texas Health Science Center at Houston||Human Genetics Center School of Public Health, The University of Texas Health Science Center at HoustonDepartment of Pediatrics, Erasmus MC University Medical CenterLaboratory of Epidemiology and Population Science, National Institute on AgingDepartment of Biochemistry, Ewha Womans University School of MedicineDepartment of Genetics, University of Groningen, University Medical Center GroningenDepartment of Genetics, University of Groningen, University Medical Center GroningenDepartment of Internal Medicine, Erasmus MC University Medical Center||The Generation R Study, Erasmus MC University Medical CenterCOPSAC, Copenhagen University Hospital, Herlev-GentofteNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of CopenhagenAvera Institute of Human Genetics, Avera McKennan Hospital & University Health CenterDepartment of Microbiology and Immunology, Rega Instituut||Center for MicrobiologyInstitute for Community Medicine, University Medicine GreifswaldGenetics and Genome Biology, The Hospital for Sick Children Research InstituteDepartment of Medicine, University of Toronto||Division of Gastroenterology, Mount Sinai HospitalMRC Integrative Epidemiology Unit, University of Bristol||Population Health Sciences, Bristol Medical SchoolDepartment of Internal Medicine, Erasmus MC University Medical CenterSchool of Public Health, Harvard UniversityDepartment of Biology, University of CopenhagenDepartment of Twin Research & Genetic EpidemiologyInstitute of Clinical Molecular Biology, Kiel UniversityDepartment of Psychiatry, Radboudumc, Donders Institute for Brain, Cognition and BehaviourMRC Integrative Epidemiology Unit, University of Bristol||Population Health Sciences, Bristol Medical SchoolMRC Integrative Epidemiology Unit, University of Bristol||Population Health Sciences, Bristol Medical SchoolDepartment of Genetics, University of Groningen, University Medical Center Groningen||Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO UniversityInstitute of Clinical Molecular Biology, Kiel University||Division of Public Health Sciences, Fred Hutchinson Cancer Research CenterDepartment of Genetics, University of Groningen, University Medical Center GroningenDepartment of Epidemiology, Erasmus MC University Medical Center||Nuffield Department of Population Health, University of OxfordDepartment of Computer Science and Cell Biology, Weizmann Institute of ScienceNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of CopenhagenDepartment of Medicine I, University Hospital Schleswig-HolsteinDepartment of Nutrition, University of North Carolina at Chapel Hill||Nutrition Research Institute, University of North Carolina at Chapel HillDivision of Gastroenterology-Hepatology, Maastricht University Medical Center+||NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht UniversityCOPSAC, Copenhagen University Hospital, Herlev-GentofteDepartment of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine GreifswaldDepartment of Microbiology and Immunology, Rega Instituut||Center for MicrobiologyBiological Psychology, Vrije Universiteit||Amsterdam Public HealthAvera Institute of Human Genetics, Avera McKennan Hospital & University Health Center||Biological Psychology, Vrije UniversiteitDivision of Family Medicine and Primary Care, Department of Neurobiology, Care Sciences and Society, Karolinska InstitutetDepartment of Human Genetics, University of California||Department of Medicine, University of CaliforniaDepartment of Medicine A, University Medicine GreifswaldStress Research Institute, Stockholm UniversityInstitute of Clinical Medicine, Internal Medicine, University of Eastern FinlandDepartment of Medicine, University of TorontoDepartment of Genetics, University of Groningen, University Medical Center GroningenDepartment of Genetics, University of Groningen, University Medical Center Groningen||Istituto di Ricerca Genetica e Biomedica, National Research CouncilDepartment of Neurology, University of Alabama at BirminghamEstonian Genome Centre, Institute of Genomics, University of TartuDepartment of Pediatrics, University of California San Diego||Center for Microbiome Innovation, University of California San Diego||Center for Microbiome Innovation and department of Bioengeering, University of California San DiegoDepartment of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine GreifswaldDepartment of Microbiology and Immunology, Rega Instituut||Center for MicrobiologyDepartment of Medicine, University of Toronto||Division of Gastroenterology, Mount Sinai HospitalDepartment of Epidemiology and Population Health, Albert Einstein College of MedicineInstitute of Clinical Molecular Biology, Kiel UniversityDepartment of Twin Research & Genetic EpidemiologyThe Generation R Study, Erasmus MC University Medical Center||Department of Epidemiology, Erasmus MC University Medical CenterDepartment of Endocrinology, Amsterdam University Medical CenterDepartment of Neurology, University of Alabama at BirminghamDepartment of Biostatistics and Center for Statistical Genetics, University of MichiganDepartment of Genetics, University of Groningen, University Medical Center Groningen||Department of Pediatrics, University of Groningen, University Medical Center GroningenDivision of Gastroenterology-Hepatology, Maastricht University Medical Center+||NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht UniversityNovo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of CopenhagenBiological Psychology, Vrije Universiteit

10.1101/2020.06.26.173724

遗传学微生物学分子生物学

J?rgensen Torben,van der Graaf Adriaan,Demirkan Ayse,Lieb Wolfgang,Kraaij Robert,Raes Jeroen,Stokholm Jakob,Org Elin,Spector Tim D.,Uitterlinden Andre G.,Franke Andre,Zhernakova Alexandra,Kim Han-Na,Barkan Elad,Shah Shiraz A.,Kurilshikov Alexander,Medina-Gomez Carolina,Bacigalupe Rodrigo,Wang Jun,Liu Xingrong,Hansen Tue H.,Frost Fabian,Turpin Williams,Vieira-Silva Sara,V?sa Urmo,Walter Susanna,Watanabe Kyoko,Weiss Stefan,Weiss Frank U.,Willemsen Gonneke,Jonkers Daisy M.A.E.,Vasquez Alejandro Arias,Jackson Matthew A.,Mujagic Zlatan,Qibin Qi,Rothschild Daphna,Shin Hocheol,Steves Claire J.,D?ˉAmato Mauro,Duijts Liesbeth,Burk Robert D.,Claringbould Annique,Fornage Myriam,Moll Henriette A.,Launer Lenore J.,Kim Hyung-Lae,Westra Harm-Jan,Wijmenga Cisca,Rivadeneira Fernando,Thorsen Jonathan,Hansen Torben,Finnicum Casey T.,Tito Raul Y.,V?lzke Henry,Paterson Andrew D.,Croitoru Kenneth,Wade Kaitlin H.,Radjabzadeh Djawad,Weissbrod Omer,S?rensen S?ren J.,Le Roy Caroline I.,R¨1hlemann Malte C.,Szopinska-Tokov Joanna,Hughes David A.,Timpson Nicholas J.,Zhernakova Daria V.,Kaplan Robert C.,Franke Lude,van Duijn Cornelia M.,Segal Eran,Borisevich Dmitrii,Laudes Matthias,Meyer Katie A.,Keszthelyi Daniel,Bisgaard Hans,Homuth Georg,Joossens Marie,de Geus Eco J.C.,Davies Gareth E.,Agreus Lars,Lusis Aldons J.,Lerch Markus M.,Andreasson Anna,Laakso Markku,Bedrani Larbi,Bonder Marc Jan,Sanna Serena,Payami Haydeh,L¨1ll Kreete,Knight Rob,V?lker Uwe,Falony Gwen,Raygoza Garay Juan Antonio,Moon Jee-Young,Bang Corinna,Bell Jordana T.,Jaddoe Vincent W.V.,Ijzerman Richard G.,Wallen Zachary D.,Boehnke Michael,Fu Jingyuan,Masclee Ad A.M.,Pedersen Oluf,Boomsma Dorret I..Genetics of human gut microbiome composition[EB/OL].(2025-03-28)[2025-08-02].https://www.biorxiv.org/content/10.1101/2020.06.26.173724.点此复制

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