Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases.
database
gut microbe
metagenome-assembled genome
prokaryotic genome
viral genome
Journal
Cell genomics
ISSN: 2666-979X
Titre abrégé: Cell Genom
Pays: United States
ID NLM: 9918284260106676
Informations de publication
Date de publication:
14 Dec 2022
14 Dec 2022
Historique:
received:
05
01
2022
revised:
27
06
2022
accepted:
31
10
2022
entrez:
13
2
2023
pubmed:
14
2
2023
medline:
14
2
2023
Statut:
epublish
Résumé
We reconstructed 19,084 prokaryotic and 31,395 viral genomes from 787 Japanese gut metagenomes as Japanese metagenome-assembled genomes (JMAG) and Japanese Virus Database (JVD), which are large microbial genome datasets for a single population. Population-specific enrichment of the
Identifiants
pubmed: 36778050
doi: 10.1016/j.xgen.2022.100219
pii: S2666-979X(22)00172-0
pmc: PMC9903723
doi:
Types de publication
Journal Article
Langues
eng
Pagination
100219Informations de copyright
© 2022 The Author(s).
Déclaration de conflit d'intérêts
The authors declare no competing interests.
Références
Nat Med. 2019 Apr;25(4):679-689
pubmed: 30936547
Nature. 2019 May;569(7758):655-662
pubmed: 31142855
Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1702-7
pubmed: 15653771
Science. 2018 Nov 2;362(6414):510-511
pubmed: 30385553
Nat Hum Behav. 2020 Mar;4(3):308-316
pubmed: 31959922
Cell Host Microbe. 2020 Sep 9;28(3):380-389.e9
pubmed: 32652061
Cell Rep. 2022 Jan 11;38(2):110204
pubmed: 35021085
Trends Microbiol. 2018 Nov;26(11):943-954
pubmed: 29909042
Annu Rev Microbiol. 2010;64:475-93
pubmed: 20528693
Nat Commun. 2021 Feb 16;12(1):1044
pubmed: 33594055
Front Cell Infect Microbiol. 2020 Dec 11;10:585973
pubmed: 33363050
Cell Host Microbe. 2019 Feb 13;25(2):195-209
pubmed: 30763534
PeerJ. 2019 Jul 26;7:e7359
pubmed: 31388474
Microbiome. 2020 Jun 10;8(1):90
pubmed: 32522236
Nat Med. 2019 Apr;25(4):667-678
pubmed: 30936548
Nat Commun. 2020 May 25;11(1):2610
pubmed: 32451391
Nat Commun. 2018 Nov 14;9(1):4781
pubmed: 30429469
Microbiome. 2018 Feb 01;6(1):24
pubmed: 29391057
Nat Microbiol. 2018 Jul;3(7):836-843
pubmed: 29807988
PeerJ. 2015 May 28;3:e985
pubmed: 26038737
Nat Biotechnol. 2017 Nov;35(11):1026-1028
pubmed: 29035372
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Mol Biol Evol. 2021 Dec 9;38(12):5825-5829
pubmed: 34597405
BMC Genomics. 2010 Apr 16;11:243
pubmed: 20398357
Cell Syst. 2016 Dec 21;3(6):572-584.e3
pubmed: 27818083
Cell Host Microbe. 2019 Nov 13;26(5):666-679.e7
pubmed: 31607556
BMC Bioinformatics. 2007 Jun 18;8:209
pubmed: 17577412
Microbiome. 2021 Apr 12;9(1):89
pubmed: 33845877
Bioinformatics. 2016 Feb 15;32(4):605-7
pubmed: 26515820
Nat Biotechnol. 2021 May;39(5):578-585
pubmed: 33349699
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Ann Rheum Dis. 2021 Dec;80(12):1575-1583
pubmed: 34426398
Nucleic Acids Res. 2017 Jan 4;45(D1):D491-D498
pubmed: 27789703
Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):E6166-E6175
pubmed: 28696303
Elife. 2018 May 30;7:
pubmed: 29846171
Curr Protoc Bioinformatics. 2020 Jun;70(1):e102
pubmed: 32559359
Arch Virol. 2021 Sep;166(9):2633-2648
pubmed: 34231026
Nat Methods. 2014 Nov;11(11):1144-6
pubmed: 25218180
ISME J. 2017 Dec;11(12):2864-2868
pubmed: 28742071
Nat Microbiol. 2017 Nov;2(11):1533-1542
pubmed: 28894102
Nat Commun. 2018 Apr 24;9(1):1631
pubmed: 29691385
Nat Commun. 2021 Feb 15;12(1):1032
pubmed: 33589587
Nat Microbiol. 2019 Feb;4(2):293-305
pubmed: 30531976
Nat Methods. 2021 Apr;18(4):366-368
pubmed: 33828273
Cell Metab. 2012 Nov 7;16(5):559-64
pubmed: 23140640
Nat Microbiol. 2021 Jul;6(7):960-970
pubmed: 34168315
Nucleic Acids Res. 2019 Jul 2;47(W1):W256-W259
pubmed: 30931475
Nat Commun. 2014 Jul 24;5:4498
pubmed: 25058116
Nat Genet. 2021 Oct;53(10):1415-1424
pubmed: 34594039
Microbiome. 2017 Jul 6;5(1):69
pubmed: 28683828
Nat Biotechnol. 2019 Feb;37(2):179-185
pubmed: 30718868
Front Cell Infect Microbiol. 2020 Sep 10;10:481
pubmed: 33014897
Ann Rheum Dis. 2022 Feb;81(2):278-288
pubmed: 34880054
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Nat Microbiol. 2018 Jan;3(1):38-46
pubmed: 29133882
Cell Host Microbe. 2020 Nov 11;28(5):724-740.e8
pubmed: 32841606
Cell. 2015 Jan 29;160(3):447-60
pubmed: 25619688
Stroke. 2022 Mar;53(3):895-903
pubmed: 34727738
Ann Rheum Dis. 2020 Jan;79(1):103-111
pubmed: 31699813
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
Gigascience. 2019 Mar 1;8(3):
pubmed: 30698687
PLoS Comput Biol. 2018 Jan 26;14(1):e1005944
pubmed: 29373581
Cell Host Microbe. 2019 Feb 13;25(2):261-272.e5
pubmed: 30763537
Cell. 2021 Feb 18;184(4):1098-1109.e9
pubmed: 33606979
Nature. 2019 Apr;568(7753):499-504
pubmed: 30745586
BMC Microbiol. 2016 Nov 28;16(1):284
pubmed: 27894251
Genome Res. 2015 Jul;25(7):1043-55
pubmed: 25977477
Am J Hum Genet. 2007 Sep;81(3):559-75
pubmed: 17701901
Nature. 2010 Jul 15;466(7304):334-8
pubmed: 20631792
Nat Biotechnol. 2021 Jun;39(6):727-736
pubmed: 33462508
Cell. 2019 Jan 24;176(3):649-662.e20
pubmed: 30661755
Nucleic Acids Res. 2002 Apr 1;30(7):1575-84
pubmed: 11917018
NPJ Biofilms Microbiomes. 2016 Jul 06;2:16010
pubmed: 28721247
Nat Genet. 2006 Aug;38(8):904-9
pubmed: 16862161
Nature. 2010 Apr 8;464(7290):908-12
pubmed: 20376150
Int J Syst Evol Microbiol. 2012 Aug;62(Pt 8):1992-1996
pubmed: 22003038
Nat Biotechnol. 2019 Feb;37(2):186-192
pubmed: 30718869
BMC Bioinformatics. 2010 Mar 08;11:119
pubmed: 20211023
Nat Med. 2019 Jun;25(6):968-976
pubmed: 31171880
Nat Med. 2019 Sep;25(9):1442-1452
pubmed: 31477907
Nucleic Acids Res. 2000 Jan 1;28(1):27-30
pubmed: 10592173
Cell Host Microbe. 2019 Dec 11;26(6):764-778.e5
pubmed: 31757768
Bioinformatics. 2011 Mar 15;27(6):863-4
pubmed: 21278185
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
DNA Res. 2016 Apr;23(2):125-33
pubmed: 26951067
Nat Methods. 2017 Jun;14(6):587-589
pubmed: 28481363
Nucleic Acids Res. 2021 Sep 20;49(16):9077-9096
pubmed: 34417604
Bioinformatics. 2019 Nov 15;:
pubmed: 31730192
Viruses. 2021 Aug 06;13(8):
pubmed: 34452423
Cell Host Microbe. 2020 Nov 11;28(5):741-751.e4
pubmed: 32910902
Genome Biol. 2016 Jun 20;17(1):132
pubmed: 27323842
Nature. 2019 Apr;568(7753):505-510
pubmed: 30867587
Nat Commun. 2020 Mar 31;11(1):1612
pubmed: 32235826
J Exp Med. 2022 Jul 4;219(7):
pubmed: 35608941
Bioinformatics. 2014 Jul 15;30(14):2068-9
pubmed: 24642063
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
pubmed: 15034147
Nat Biotechnol. 2017 Aug 8;35(8):725-731
pubmed: 28787424
Front Microbiol. 2016 Mar 31;7:455
pubmed: 27065999
Nat Biotechnol. 2019 Jun;37(6):632-639
pubmed: 31061483
Nat Biotechnol. 2021 Jan;39(1):105-114
pubmed: 32690973
Nucleic Acids Res. 2018 Jul 2;46(W1):W95-W101
pubmed: 29771380