Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort.

ABO Blood-Group System / genetics Bifidobacterium / physiology Clostridiales / physiology Cohort Studies Colorectal Neoplasms / genetics Depressive Disorder, Major / genetics Diet Dietary Fiber Enterococcus faecalis / physiology Gastrointestinal Microbiome / genetics Gastrointestinal Tract / microbiology Genetic Variation Genome-Wide Association Study Host Microbial Interactions Humans Lactase / genetics Mediator Complex / genetics Mendelian Randomization Analysis Metagenome Morganella / physiology Polymorphism, Single Nucleotide

Journal

Nature genetics
ISSN: 1546-1718
Titre abrégé: Nat Genet
Pays: United States
ID NLM: 9216904

Informations de publication

Date de publication:
02 2022
Historique:
received: 21 10 2020
accepted: 19 11 2021
pubmed: 5 2 2022
medline: 26 2 2022
entrez: 4 2 2022
Statut: ppublish

Résumé

Human genetic variation affects the gut microbiota through a complex combination of environmental and host factors. Here we characterize genetic variations associated with microbial abundances in a single large-scale population-based cohort of 5,959 genotyped individuals with matched gut microbial metagenomes, and dietary and health records (prevalent and follow-up). We identified 567 independent SNP-taxon associations. Variants at the LCT locus associated with Bifidobacterium and other taxa, but they differed according to dairy intake. Furthermore, levels of Faecalicatena lactaris associated with ABO, and suggested preferential utilization of secreted blood antigens as energy source in the gut. Enterococcus faecalis levels associated with variants in the MED13L locus, which has been linked to colorectal cancer. Mendelian randomization analysis indicated a potential causal effect of Morganella on major depressive disorder, consistent with observational incident disease analysis. Overall, we identify and characterize the intricate nature of host-microbiota interactions and their association with disease.

Identifiants

DOI: 10.1038/s41588-021-00991-z PMID: 35115689 PMC: PMC9883041
pubmed: 35115689
doi: 10.1038/s41588-021-00991-z
pii: 10.1038/s41588-021-00991-z
pmc: PMC9883041
mid: NIHMS1852049
doi:

Substances chimiques

ABO Blood-Group System 0
Dietary Fiber 0
MED13L protein, human 0
Mediator Complex 0
Lactase EC 3.2.1.108

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

134-142

Subventions

Organisme : NCATS NIH HHS
ID : UL1 TR001442
Pays : United States
Organisme : NIEHS NIH HHS
ID : P42 ES010337
Pays : United States
Organisme : British Heart Foundation
ID : RG/18/13/33946
Pays : United Kingdom
Organisme : NIDDK NIH HHS
ID : P30 DK120515
Pays : United States
Organisme : Medical Research Council
Pays : United Kingdom
Organisme : NIDDK NIH HHS
ID : R01 DK124318
Pays : United States
Organisme : NIDDK NIH HHS
ID : U01 DK061734
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NIDDK NIH HHS
ID : R01 DK121378
Pays : United States
Organisme : Chief Scientist Office
Pays : United Kingdom
Organisme : British Heart Foundation
ID : RG/13/13/30194
Pays : United Kingdom
Organisme : NIDDK NIH HHS
ID : R01 DK106419
Pays : United States

Informations de copyright

© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.

Références

Lab Anim Sci. 1998 Jun;48(3):253-5
pubmed: 10090024
J Nutr. 2008 Jan;138(1):226S-234S
pubmed: 18156429
FEMS Microbiol Rev. 2017 Mar 1;41(2):182-199
pubmed: 28364729
Front Genet. 2013 Dec 23;4:297
pubmed: 24391664
Cell Host Microbe. 2016 May 11;19(5):731-43
pubmed: 27173935
Nat Commun. 2021 May 11;12(1):2671
pubmed: 33976176
PLoS One. 2014 Mar 11;9(3):e90731
pubmed: 24618913
Nat Genet. 2015 Mar;47(3):284-90
pubmed: 25642633
N Engl J Med. 2020 Oct 15;383(16):1522-1534
pubmed: 32558485
Nat Genet. 2021 Feb;53(2):156-165
pubmed: 33462485
Genetics. 2015 Feb;199(2):267-79
pubmed: 25657345
Res Microbiol. 2021 Sep-Oct;172(6):103851
pubmed: 34186167
Genome Med. 2018 Jan 29;10(1):6
pubmed: 29378630
Trends Neurosci. 2013 May;36(5):305-12
pubmed: 23384445
Dig Dis Sci. 2016 Jun;61(6):1461-72
pubmed: 26725064
PLoS One. 2010 Feb 02;5(2):e9009
pubmed: 20126401
Nat Rev Immunol. 2017 Apr;17(4):219-232
pubmed: 28260787
Gut Microbes. 2018 Jan 2;9(1):68-75
pubmed: 28816579
Antonie Van Leeuwenhoek. 2018 Jun;111(6):859-873
pubmed: 29460206
J Biol Chem. 2008 Mar 28;283(13):8545-54
pubmed: 18227066
Nutrients. 2015 Aug 13;7(8):6751-79
pubmed: 26287234
Nat Med. 2020 Apr;26(4):549-557
pubmed: 32273609
Nat Biotechnol. 2018 Nov;36(10):996-1004
pubmed: 30148503
Cell Syst. 2016 Dec 21;3(6):572-584.e3
pubmed: 27818083
Cell Metab. 2022 May 3;34(5):719-730.e4
pubmed: 35354069
PLoS Genet. 2008 Jul 04;4(7):e1000118
pubmed: 18604267
Nat Genet. 2012 Jul 22;44(8):955-9
pubmed: 22820512
Philos Trans R Soc Lond B Biol Sci. 2011 Mar 27;366(1566):863-77
pubmed: 21320900
Nat Ecol Evol. 2018 Jun;2(6):936-943
pubmed: 29662222
Brain Behav Immun. 2015 Aug;48:186-94
pubmed: 25882912
Nature. 2020 May;581(7809):434-443
pubmed: 32461654
Elife. 2018 May 30;7:
pubmed: 29846171
Gigascience. 2015 Feb 25;4:7
pubmed: 25722852
Nat Genet. 2016 Nov;48(11):1396-1406
pubmed: 27723756
Nat Neurosci. 2019 Mar;22(3):353-361
pubmed: 30692689
Nat Genet. 2012 Mar 18;44(4):369-75, S1-3
pubmed: 22426310
Heredity (Edinb). 2005 Sep;95(3):221-7
pubmed: 16077740
Bioinformatics. 2017 Sep 01;33(17):2776-2778
pubmed: 28475694
Nat Neurosci. 2017 Feb;20(2):145-155
pubmed: 28092661
PLoS One. 2012;7(6):e28742
pubmed: 22719820
PLoS One. 2011;6(5):e20113
pubmed: 21625510
Nat Rev Microbiol. 2019 Mar;17(3):194
pubmed: 30538306
Clin Exp Gastroenterol. 2012;5:113-21
pubmed: 22826639
Front Microbiol. 2017 Nov 15;8:2224
pubmed: 29187837
Gut Microbes. 2021 Jan-Dec;13(1):1-22
pubmed: 33651661
Nature. 2014 Jan 23;505(7484):559-63
pubmed: 24336217
Nat Ecol Evol. 2016 Dec 05;1(1):15
pubmed: 28812567
Trends Microbiol. 2016 May;24(5):402-413
pubmed: 26996765
Genome Res. 2016 Dec;26(12):1721-1729
pubmed: 27852649
Genome Biol. 2015 Sep 15;16:191
pubmed: 26374288
Wellcome Open Res. 2019 Dec 10;4:199
pubmed: 32462081
Nucleic Acids Res. 2009 Jan;37(Database issue):D233-8
pubmed: 18838391
Nat Struct Mol Biol. 2013 May;20(5):611-9
pubmed: 23563140
Nat Genet. 2021 Feb;53(2):147-155
pubmed: 33462482
Cell. 2014 Nov 6;159(4):789-99
pubmed: 25417156
Nucleic Acids Res. 2010 Sep;38(16):e164
pubmed: 20601685
Science. 2016 Apr 29;352(6285):565-9
pubmed: 27126040
Curr Microbiol. 2017 Aug;74(8):987-995
pubmed: 28593350
Bioessays. 2013 Oct;35(10):862-7
pubmed: 23836453
Gastroenterology Res. 2018 Jun;11(3):238-240
pubmed: 29915636
Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18493-8
pubmed: 23091028
Nat Genet. 2016 Nov;48(11):1413-1417
pubmed: 27694960
Wiley Interdiscip Rev Syst Biol Med. 2016 Nov;8(6):517-535
pubmed: 27599872
Nat Commun. 2020 Jul 3;11(1):3285
pubmed: 32620774
Nat Biotechnol. 2020 Sep;38(9):1079-1086
pubmed: 32341564
Am J Hum Genet. 2004 Apr;74(4):765-9
pubmed: 14997420
J Clin Med. 2019 Mar 20;8(3):
pubmed: 30897751
Front Microbiol. 2015 Oct 06;6:1050
pubmed: 26500616
J Biol Chem. 2020 Jan 10;295(2):325-334
pubmed: 31792054
Microbiome. 2015 Oct 12;3:44
pubmed: 26455879
BMC Genomics. 2016 Nov 21;17(1):941
pubmed: 27871240
Gut. 2016 Feb;65(2):330-9
pubmed: 26338727
Nature. 2008 Sep 25;455(7212):547-51
pubmed: 18794900
Genes Dev. 2009 Feb 15;23(4):439-51
pubmed: 19240132
Cell Discov. 2021 Feb 9;7(1):9
pubmed: 33563976
Annu Rev Genet. 2017 Nov 27;51:413-433
pubmed: 28934590
Nat Microbiol. 2019 Apr;4(4):623-632
pubmed: 30718848
mBio. 2019 Jun 18;10(3):
pubmed: 31213556
Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15124-9
pubmed: 17008408
Int J Epidemiol. 2018 Jun 1;47(3):696-696i
pubmed: 29165699
J Infect Public Health. 2017 Sep - Oct;10(5):681-684
pubmed: 28143799
Eur J Public Health. 2015 Jun;25(3):539-46
pubmed: 25422363
Cell. 2016 Nov 17;167(5):1339-1353.e21
pubmed: 27863247
Neuro Endocrinol Lett. 2008 Feb;29(1):117-24
pubmed: 18283240
Lancet Gastroenterol Hepatol. 2017 Oct;2(10):738-746
pubmed: 28690131
Science. 2016 Apr 29;352(6285):532-5
pubmed: 27126034
Nat Genet. 2016 Nov;48(11):1407-1412
pubmed: 27694959
Curr Opin Microbiol. 2020 Aug;56:59-66
pubmed: 32663769
Nat Rev Microbiol. 2019 Mar;17(3):193
pubmed: 30542201
Cell. 2019 Jan 24;176(3):649-662.e20
pubmed: 30661755
Nat Genet. 2016 Nov;48(11):1443-1448
pubmed: 27694958
Gut. 2017 Jun;66(6):1031-1038
pubmed: 27053630
Nat Genet. 2022 Jan;54(1):52-61
pubmed: 34980918
Cell. 2019 Mar 21;177(1):26-31
pubmed: 30901543
Sci Adv. 2019 Aug 28;5(8):eaaw7696
pubmed: 31489370
Trends Immunol. 2017 Sep;38(9):633-647
pubmed: 28669638
Nat Biotechnol. 2007 Apr;25(4):454-64
pubmed: 17401360
Sci Adv. 2020 Dec 2;6(49):
pubmed: 33268363
Nat Rev Mol Cell Biol. 2015 Mar;16(3):155-66
pubmed: 25693131
Front Genet. 2015 Mar 19;6:81
pubmed: 25852737
Nat Genet. 2021 Jun;53(6):801-808
pubmed: 33888907
Nat Rev Microbiol. 2020 Jun;18(6):344-359
pubmed: 32055025
Adv Sci (Weinh). 2021 May 02;8(12):2100707
pubmed: 34194954
J Biol Chem. 2006 Dec 8;281(49):37748-57
pubmed: 16990278
Science. 2016 Apr 29;352(6285):560-4
pubmed: 27126039
Nutr Rev. 1990 Oct;48(10):373-9
pubmed: 2082216
Nat Rev Microbiol. 2018 Sep;16(9):567-576
pubmed: 29789680
Environ Microbiol. 2013 Jan;15(1):211-26
pubmed: 22891823
Microbiome. 2018 Mar 2;6(1):45
pubmed: 29499759
Carcinogenesis. 2002 Mar;23(3):529-36
pubmed: 11895869
Nat Genet. 2019 Apr;51(4):600-605
pubmed: 30778224
Nat Microbiol. 2020 Sep;5(9):1079-1087
pubmed: 32572223
Curr Biol. 2020 Nov 2;30(21):4307-4315.e13
pubmed: 32888485
Glycobiology. 2018 Dec 1;28(1):3-8
pubmed: 29040563
Nat Biotechnol. 2021 Jan;39(1):105-114
pubmed: 32690973
Gut Microbes. 2018 Jan 2;9(1):61-67
pubmed: 28767316
Nucleic Acids Res. 2018 Jul 2;46(W1):W95-W101
pubmed: 29771380
Nature. 2018 Mar 8;555(7695):210-215
pubmed: 29489753

Auteurs

Youwen Qin (Y)

Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia.
ORCID: 0000-0003-3956-4711

Aki S Havulinna (AS)

Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland.
Institute for Molecular Medicine Finland, FIMM-HiLIFE, Helsinki, Finland.
ORCID: 0000-0002-4787-8959

Yang Liu (Y)

Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia.

Pekka Jousilahti (P)

Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland.

Scott C Ritchie (SC)

Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.
ORCID: 0000-0002-8454-9548

Alex Tokolyi (A)

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
ORCID: 0000-0003-4222-7484

Jon G Sanders (JG)

Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.
Cornell Institute for Host-Microbe Interaction and Disease, Cornell University, Ithaca, NY, USA.

Liisa Valsta (L)

Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland.

Marta Brożyńska (M)

Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.

Qiyun Zhu (Q)

Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.

Anupriya Tripathi (A)

Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.

Yoshiki Vázquez-Baeza (Y)

Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
Department of Computer Science & Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
ORCID: 0000-0001-6014-2009

Rohit Loomba (R)

NAFLD Research Center, Department of Medicine, University of California San Diego, La Jolla, CA, USA.

Susan Cheng (S)

Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
ORCID: 0000-0002-4977-036X

Mohit Jain (M)

Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.

Teemu Niiranen (T)

Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland.
Department of Medicine, Turku University Hospital and University of Turku, Turku, Finland.

Leo Lahti (L)

Department of Computing, University of Turku, Turku, Finland.
ORCID: 0000-0001-5537-637X

Rob Knight (R)

Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
Department of Computer Science & Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.

Veikko Salomaa (V)

Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland.
ORCID: 0000-0001-7563-5324

Michael Inouye (M)

Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia. mi336@medschl.cam.ac.uk.
School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia. mi336@medschl.cam.ac.uk.
Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK. mi336@medschl.cam.ac.uk.
British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK. mi336@medschl.cam.ac.uk.
British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK. mi336@medschl.cam.ac.uk.
Health Data Research UK Cambridge, Wellcome Genome Campus & University of Cambridge, Cambridge, UK. mi336@medschl.cam.ac.uk.
The Alan Turing Institute, London, UK. mi336@medschl.cam.ac.uk.
ORCID: 0000-0001-9413-6520

Guillaume Méric (G)

Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia. guillaume.meric@baker.edu.au.
Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia. guillaume.meric@baker.edu.au.
ORCID: 0000-0001-6288-9958

Articles similaires

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female

Evaluation of Low-Value Services Across Major Medicare Advantage Insurers and Traditional Medicare.

Ciara Duggan, Adam L Beckman, Ishani Ganguli et al.
1.00
Humans United States Aged Cross-Sectional Studies Medicare Part C

Effectiveness of Virtual Yoga for Chronic Low Back Pain: A Randomized Clinical Trial.

Hallie Tankha, Devyn Gaskins, Amanda Shallcross et al.
1.00
Humans Yoga Low Back Pain Female Male

Classifications MeSH

questionsmedicales.fr › Facteurs biologiques › Antigènes › Isoantigènes › Antigènes de groupe sanguin › Système ABO de groupes sanguins › Combined effects of host genetics and diet on...
questionsmedicales.fr › Bactéries › Bactéries à Gram positif › Bâtonnets à Gram positif › Bâtonnets asporogènes à Gram positif › Bâtonnets asporogènes irréguliers à Gram positif › Actinobacteria › Bifidobacterium › Combined effects of host genetics and diet on...
questionsmedicales.fr › Bactéries › Firmicutes › Clostridiales › Combined effects of host genetics and diet on...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Caractéristiques des études épidémiologiques › Études épidémiologiques › Études de cohortes › Combined effects of host genetics and diet on...
questionsmedicales.fr › Maladies de l'appareil digestif › Maladies gastro-intestinales › Maladies intestinales › Maladies du rectum › Tumeurs colorectales › Combined effects of host genetics and diet on...
questionsmedicales.fr › Troubles mentaux › Troubles de l'humeur › Trouble dépressif › Trouble dépressif majeur › Combined effects of host genetics and diet on...
questionsmedicales.fr › Phénomènes physiologiques › Alimentation et nutrition › Phénomènes physiologiques nutritionnels › Régime alimentaire › Combined effects of host genetics and diet on...
questionsmedicales.fr › Aliments et boissons › Aliments › Fibre alimentaire › Combined effects of host genetics and diet on...
questionsmedicales.fr › Bactéries › Bactéries à Gram positif › Lactobacillales › Enterococcaceae › Enterococcus › Enterococcus faecalis › Combined effects of host genetics and diet on...
questionsmedicales.fr › Environnement et santé publique › Environnement › Écosystème › Biodiversité › Biote › Microbiote › Microbiome gastro-intestinal › Combined effects of host genetics and diet on...
questionsmedicales.fr › Système digestif › Tube digestif › Combined effects of host genetics and diet on...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Combined effects of host genetics and diet on...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Épidémiologie moléculaire › Étude d'association pangénomique › Combined effects of host genetics and diet on...
questionsmedicales.fr › Phénomènes biologiques › Interactions hôte-microbes › Combined effects of host genetics and diet on...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Combined effects of host genetics and diet on...
questionsmedicales.fr › Enzymes et coenzymes › Enzymes › Hydrolases › Glycosidases › Galactosidases › beta-Galactosidase › Lactase › Combined effects of host genetics and diet on...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines nucléaires › Complexe médiateur › Combined effects of host genetics and diet on...
questionsmedicales.fr › Techniques d'investigation › Analyse de randomisation mendélienne › Combined effects of host genetics and diet on...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Métagénome › Combined effects of host genetics and diet on...
questionsmedicales.fr › Bactéries › Proteobacteria › Gammaproteobacteria › Enterobacteriaceae › Morganella › Combined effects of host genetics and diet on...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Polymorphisme génétique › Polymorphisme de nucléotide simple › Combined effects of host genetics and diet on...