A genomic catalog of Earth's microbiomes.
Journal
Nature biotechnology
ISSN: 1546-1696
Titre abrégé: Nat Biotechnol
Pays: United States
ID NLM: 9604648
Informations de publication
Date de publication:
04 2021
04 2021
Historique:
received:
24
12
2019
accepted:
28
09
2020
pubmed:
11
11
2020
medline:
23
4
2021
entrez:
10
11
2020
Statut:
ppublish
Résumé
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.
Identifiants
pubmed: 33169036
doi: 10.1038/s41587-020-0718-6
pii: 10.1038/s41587-020-0718-6
pmc: PMC8041624
doi:
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
499-509Investigateurs
Helena Abreu
(H)
Silvia G Acinas
(SG)
Eric Allen
(E)
Michelle A Allen
(MA)
Lauren V Alteio
(LV)
Gary Andersen
(G)
Alexandre M Anesio
(AM)
Graeme Attwood
(G)
Viridiana Avila-Magaña
(V)
Yacine Badis
(Y)
Jake Bailey
(J)
Brett Baker
(B)
Petr Baldrian
(P)
Hazel A Barton
(HA)
David A C Beck
(DAC)
Eric D Becraft
(ED)
Harry R Beller
(HR)
J Michael Beman
(JM)
Rizlan Bernier-Latmani
(R)
Timothy D Berry
(TD)
Anthony Bertagnolli
(A)
Stefan Bertilsson
(S)
Jennifer M Bhatnagar
(JM)
Jordan T Bird
(JT)
Jeffrey L Blanchard
(JL)
Sara E Blumer-Schuette
(SE)
Brendan Bohannan
(B)
Mikayla A Borton
(MA)
Allyson Brady
(A)
Susan H Brawley
(SH)
Juliet Brodie
(J)
Steven Brown
(S)
Jennifer R Brum
(JR)
Andreas Brune
(A)
Donald A Bryant
(DA)
Alison Buchan
(A)
Daniel H Buckley
(DH)
Joy Buongiorno
(J)
Hinsby Cadillo-Quiroz
(H)
Sean M Caffrey
(SM)
Ashley N Campbell
(AN)
Barbara Campbell
(B)
Stephanie Carr
(S)
JoLynn Carroll
(J)
S Craig Cary
(SC)
Anna M Cates
(AM)
Rose Ann Cattolico
(RA)
Ricardo Cavicchioli
(R)
Ludmila Chistoserdova
(L)
Maureen L Coleman
(ML)
Philippe Constant
(P)
Jonathan M Conway
(JM)
Walter P Mac Cormack
(WP)
Sean Crowe
(S)
Byron Crump
(B)
Cameron Currie
(C)
Rebecca Daly
(R)
Kristen M DeAngelis
(KM)
Vincent Denef
(V)
Stuart E Denman
(SE)
Adey Desta
(A)
Hebe Dionisi
(H)
Jeremy Dodsworth
(J)
Nina Dombrowski
(N)
Timothy Donohue
(T)
Mark Dopson
(M)
Timothy Driscoll
(T)
Peter Dunfield
(P)
Christopher L Dupont
(CL)
Katherine A Dynarski
(KA)
Virginia Edgcomb
(V)
Elizabeth A Edwards
(EA)
Mostafa S Elshahed
(MS)
Israel Figueroa
(I)
Beverly Flood
(B)
Nathaniel Fortney
(N)
Caroline S Fortunato
(CS)
Christopher Francis
(C)
Claire M M Gachon
(CMM)
Sarahi L Garcia
(SL)
Maria C Gazitua
(MC)
Terry Gentry
(T)
Lena Gerwick
(L)
Javad Gharechahi
(J)
Peter Girguis
(P)
John Gladden
(J)
Mary Gradoville
(M)
Stephen E Grasby
(SE)
Kelly Gravuer
(K)
Christen L Grettenberger
(CL)
Robert J Gruninger
(RJ)
Jiarong Guo
(J)
Mussie Y Habteselassie
(MY)
Steven J Hallam
(SJ)
Roland Hatzenpichler
(R)
Bela Hausmann
(B)
Terry C Hazen
(TC)
Brian Hedlund
(B)
Cynthia Henny
(C)
Lydie Herfort
(L)
Maria Hernandez
(M)
Olivia S Hershey
(OS)
Matthias Hess
(M)
Emily B Hollister
(EB)
Laura A Hug
(LA)
Dana Hunt
(D)
Janet Jansson
(J)
Jessica Jarett
(J)
Vitaly V Kadnikov
(VV)
Charlene Kelly
(C)
Robert Kelly
(R)
William Kelly
(W)
Cheryl A Kerfeld
(CA)
Jeff Kimbrel
(J)
Jonathan L Klassen
(JL)
Konstantinos T Konstantinidis
(KT)
Laura L Lee
(LL)
Wen-Jun Li
(WJ)
Andrew J Loder
(AJ)
Alexander Loy
(A)
Mariana Lozada
(M)
Barbara MacGregor
(B)
Cara Magnabosco
(C)
Aline Maria da Silva
(A)
R Michael McKay
(RM)
Katherine McMahon
(K)
Chris S McSweeney
(CS)
Mónica Medina
(M)
Laura Meredith
(L)
Jessica Mizzi
(J)
Thomas Mock
(T)
Lily Momper
(L)
Mary Ann Moran
(MA)
Connor Morgan-Lang
(C)
Duane Moser
(D)
Gerard Muyzer
(G)
David Myrold
(D)
Maisie Nash
(M)
Camilla L Nesbø
(CL)
Anthony P Neumann
(AP)
Rebecca B Neumann
(RB)
Daniel Noguera
(D)
Trent Northen
(T)
Jeanette Norton
(J)
Brent Nowinski
(B)
Klaus Nüsslein
(K)
Michelle A O'Malley
(MA)
Rafael S Oliveira
(RS)
Valeria Maia de Oliveira
(V)
Tullis Onstott
(T)
Jay Osvatic
(J)
Yang Ouyang
(Y)
Maria Pachiadaki
(M)
Jacob Parnell
(J)
Laila P Partida-Martinez
(LP)
Kabir G Peay
(KG)
Dale Pelletier
(D)
Xuefeng Peng
(X)
Michael Pester
(M)
Jennifer Pett-Ridge
(J)
Sari Peura
(S)
Petra Pjevac
(P)
Alvaro M Plominsky
(AM)
Anja Poehlein
(A)
Phillip B Pope
(PB)
Nikolai Ravin
(N)
Molly C Redmond
(MC)
Rebecca Reiss
(R)
Virginia Rich
(V)
Christian Rinke
(C)
Jorge L Mazza Rodrigues
(JLM)
William Rodriguez-Reillo
(W)
Karen Rossmassler
(K)
Joshua Sackett
(J)
Ghasem Hosseini Salekdeh
(GH)
Scott Saleska
(S)
Matthew Scarborough
(M)
Daniel Schachtman
(D)
Christopher W Schadt
(CW)
Matthew Schrenk
(M)
Alexander Sczyrba
(A)
Aditi Sengupta
(A)
Joao C Setubal
(JC)
Ashley Shade
(A)
Christine Sharp
(C)
David H Sherman
(DH)
Olga V Shubenkova
(OV)
Isabel Natalia Sierra-Garcia
(IN)
Rachel Simister
(R)
Holly Simon
(H)
Sara Sjöling
(S)
Joan Slonczewski
(J)
Rafael Soares Correa de Souza
(RS)
John R Spear
(JR)
James C Stegen
(JC)
Ramunas Stepanauskas
(R)
Frank Stewart
(F)
Garret Suen
(G)
Matthew Sullivan
(M)
Dawn Sumner
(D)
Brandon K Swan
(BK)
Wesley Swingley
(W)
Jonathan Tarn
(J)
Gordon T Taylor
(GT)
Hanno Teeling
(H)
Memory Tekere
(M)
Andreas Teske
(A)
Torsten Thomas
(T)
Cameron Thrash
(C)
James Tiedje
(J)
Claire S Ting
(CS)
Benjamin Tully
(B)
Gene Tyson
(G)
Osvlado Ulloa
(O)
David L Valentine
(DL)
Marc W Van Goethem
(MW)
Jean VanderGheynst
(J)
Tobin J Verbeke
(TJ)
John Vollmers
(J)
Aurèle Vuillemin
(A)
Nicholas B Waldo
(NB)
David A Walsh
(DA)
Bart C Weimer
(BC)
Thea Whitman
(T)
Paul van der Wielen
(P)
Michael Wilkins
(M)
Timothy J Williams
(TJ)
Ben Woodcroft
(B)
Jamie Woolet
(J)
Kelly Wrighton
(K)
Jun Ye
(J)
Erica B Young
(EB)
Noha H Youssef
(NH)
Feiqiao Brian Yu
(FB)
Tamara I Zemskaya
(TI)
Ryan Ziels
(R)
Commentaires et corrections
Type : ErratumIn
Type : ErratumIn
Références
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Cell. 2019 Dec 12;179(7):1623-1635.e11
pubmed: 31835036
Nat Commun. 2013;4:2120
pubmed: 23979677
Nat Prod Rep. 2017 Feb 1;34(2):135-160
pubmed: 27907217
Science. 2017 Aug 11;357(6351):
pubmed: 28798101
Sci Data. 2018 Jan 16;5:170203
pubmed: 29337314
Nat Rev Microbiol. 2015 Apr;13(4):217-29
pubmed: 25730701
Genome Res. 2016 Nov;26(11):1612-1625
pubmed: 27803195
mBio. 2016 May 17;7(3):
pubmed: 27190214
J Bacteriol. 2005 Sep;187(18):6258-64
pubmed: 16159757
Nucleic Acids Res. 2020 Jan 8;48(D1):D454-D458
pubmed: 31612915
PeerJ. 2015 May 28;3:e985
pubmed: 26038737
Nat Methods. 2017 Nov;14(11):1063-1071
pubmed: 28967888
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):E2401-E2410
pubmed: 28265094
Nat Biotechnol. 2018 Nov;36(10):996-1004
pubmed: 30148503
BMC Bioinformatics. 2007 Jun 18;8:209
pubmed: 17577412
Science. 2017 Mar 31;355(6332):1436-1440
pubmed: 28360330
Nucleic Acids Res. 2019 Jan 8;47(D1):D678-D686
pubmed: 30407573
Nat Commun. 2019 Oct 8;10(1):4574
pubmed: 31594929
Nature. 2004 Mar 4;428(6978):37-43
pubmed: 14961025
Nucleic Acids Res. 2015 Aug 18;43(14):6761-71
pubmed: 26150420
Nat Chem Biol. 2020 Jan;16(1):60-68
pubmed: 31768033
Nucleic Acids Res. 1997 Mar 1;25(5):955-64
pubmed: 9023104
Nat Commun. 2018 Nov 27;9(1):4999
pubmed: 30479325
BMC Genomics. 2017 Jul 10;18(1):521
pubmed: 28693474
Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4904-9
pubmed: 24632729
FEMS Microbiol Rev. 2001 Jan;25(1):39-67
pubmed: 11152940
Microbiome. 2018 Sep 19;6(1):168
pubmed: 30231921
Nature. 2013 Jul 25;499(7459):431-7
pubmed: 23851394
Nat Microbiol. 2018 Mar;3(3):328-336
pubmed: 29379208
J Bacteriol. 2013 Sep;195(17):3914-24
pubmed: 23813730
Nat Commun. 2018 Feb 28;9(1):870
pubmed: 29491419
Nat Microbiol. 2017 Nov;2(11):1533-1542
pubmed: 28894102
Genome Res. 2011 Mar;21(3):487-93
pubmed: 21209072
Genome Res. 2019 Aug;29(8):1352-1362
pubmed: 31160374
Nat Microbiol. 2019 Apr;4(4):595-602
pubmed: 30833728
Nat Microbiol. 2019 Nov;4(11):1895-1906
pubmed: 31332386
Science. 2010 May 21;328(5981):994-9
pubmed: 20489017
Science. 2015 Oct 23;350(6259):434-8
pubmed: 26494757
mSystems. 2018 Apr 10;3(3):
pubmed: 29657970
Arch Public Health. 2018 Jan 6;76:2
pubmed: 29321921
Nat Commun. 2016 Oct 24;7:13219
pubmed: 27774985
Nature. 2018 Feb 1;554(7690):118-122
pubmed: 29364876
BMC Bioinformatics. 2007 Jan 20;8:18
pubmed: 17239253
PLoS Comput Biol. 2011 Oct;7(10):e1002195
pubmed: 22039361
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Bioinformatics. 2015 Jun 15;31(12):i35-43
pubmed: 26072503
Nature. 2017 Dec 21;552(7685):400-403
pubmed: 29211716
Nat Commun. 2017 Nov 10;8(1):1424
pubmed: 29127284
ISME J. 2020 May;14(5):1247-1259
pubmed: 32047279
Nature. 2018 May;557(7703):101-105
pubmed: 29695865
PLoS One. 2013 Oct 17;8(10):e77033
pubmed: 24146954
mSystems. 2018 Oct 2;3(5):
pubmed: 30320215
Nucleic Acids Res. 2020 Jan 8;48(D1):D422-D430
pubmed: 31665416
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
Stand Genomic Sci. 2016 Feb 24;11:17
pubmed: 26918089
Nucleic Acids Res. 2019 Jan 8;47(D1):D649-D659
pubmed: 30357420
Nucleic Acids Res. 2018 Jan 4;46(D1):D335-D342
pubmed: 29112718
PLoS Comput Biol. 2018 Jan 26;14(1):e1005944
pubmed: 29373581
Bioinformatics. 2009 Aug 1;25(15):1972-3
pubmed: 19505945
Nature. 2019 Apr;568(7753):499-504
pubmed: 30745586
Nucleic Acids Res. 2019 Jan 8;47(D1):D666-D677
pubmed: 30289528
Genome Res. 2015 Jul;25(7):1043-55
pubmed: 25977477
PLoS One. 2010 Mar 10;5(3):e9490
pubmed: 20224823
Cell. 2019 Jan 24;176(3):649-662.e20
pubmed: 30661755
Nat Biotechnol. 2017 Jul;35(7):676-683
pubmed: 28604660
Nature. 2018 Jun;558(7710):440-444
pubmed: 29899444
Nature. 2015 Jul 9;523(7559):208-11
pubmed: 26083755
Nat Med. 2019 Sep;25(9):1442-1452
pubmed: 31477907
Nature. 2018 Aug;560(7716):49-54
pubmed: 30013118
Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19126-31
pubmed: 19855009
Bioinformatics. 2009 May 15;25(10):1335-7
pubmed: 19307242
Nature. 2009 Dec 24;462(7276):1056-60
pubmed: 20033048
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Nat Microbiol. 2019 Apr;4(4):603-613
pubmed: 30833729
Nat Biotechnol. 2018 Jul 6;36(7):566-569
pubmed: 29979655
Bioinformatics. 2019 Nov 15;:
pubmed: 31730192
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45
pubmed: 26553804
Genome Biol. 2016 Jun 20;17(1):132
pubmed: 27323842
Nature. 2019 Apr;568(7753):505-510
pubmed: 30867587
Sci Rep. 2016 Sep 27;6:33964
pubmed: 27670777
BMC Bioinformatics. 2009 Dec 15;10:421
pubmed: 20003500
Nat Commun. 2019 Dec 2;10(1):5477
pubmed: 31792218
Nat Biotechnol. 2017 Aug 8;35(8):725-731
pubmed: 28787424
PeerJ. 2015 Aug 27;3:e1165
pubmed: 26336640
Nucleic Acids Res. 2019 Jul 2;47(W1):W81-W87
pubmed: 31032519