1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses.
Journal
Nature biotechnology
ISSN: 1546-1696
Titre abrégé: Nat Biotechnol
Pays: United States
ID NLM: 9604648
Informations de publication
Date de publication:
02 2019
02 2019
Historique:
received:
26
10
2017
accepted:
13
12
2018
entrez:
6
2
2019
pubmed:
6
2
2019
medline:
13
4
2019
Statut:
ppublish
Résumé
Reference genomes are essential for metagenomic analyses and functional characterization of the human gut microbiota. We present the Culturable Genome Reference (CGR), a collection of 1,520 nonredundant, high-quality draft genomes generated from >6,000 bacteria cultivated from fecal samples of healthy humans. Of the 1,520 genomes, which were chosen to cover all major bacterial phyla and genera in the human gut, 264 are not represented in existing reference genome catalogs. We show that this increase in the number of reference bacterial genomes improves the rate of mapping metagenomic sequencing reads from 50% to >70%, enabling higher-resolution descriptions of the human gut microbiome. We use the CGR genomes to annotate functions of 338 bacterial species, showing the utility of this resource for functional studies. We also carry out a pan-genome analysis of 38 important human gut species, which reveals the diversity and specificity of functional enrichment between their core and dispensable genomes.
Identifiants
pubmed: 30718868
doi: 10.1038/s41587-018-0008-8
pii: 10.1038/s41587-018-0008-8
pmc: PMC6784896
doi:
Substances chimiques
RNA, Ribosomal, 16S
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
179-185Commentaires et corrections
Type : CommentIn
Références
Nucleic Acids Res. 2017 Jan 4;45(D1):D566-D573
pubmed: 27789705
Nucleic Acids Res. 2016 Jul 8;44(W1):W242-5
pubmed: 27095192
Nature. 2010 Mar 4;464(7285):59-65
pubmed: 20203603
J Microbiol Methods. 2000 Oct;42(2):175-84
pubmed: 11018274
J Diabetes Investig. 2018 Jan;9(1):5-12
pubmed: 28390093
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
FEMS Microbiol Rev. 2014 Sep;38(5):996-1047
pubmed: 24861948
Nature. 2013 Aug 29;500(7464):541-6
pubmed: 23985870
Environ Microbiol. 2010 Feb;12(2):304-14
pubmed: 19807780
Int J Syst Evol Microbiol. 2012 Mar;62(Pt 3):716-721
pubmed: 22140171
Nat Microbiol. 2016 Nov 07;1:16203
pubmed: 27819657
Bioinformatics. 2006 Jul 1;22(13):1658-9
pubmed: 16731699
Biochem Soc Trans. 1999 Feb;27(2):304-8
pubmed: 10093753
Mol Biosyst. 2014 Jul 29;10(9):2441-7
pubmed: 24994036
Semin Immunopathol. 2015 Jan;37(1):5-16
pubmed: 25338280
Methods Mol Biol. 2014;1079:155-70
pubmed: 24170401
Nat Rev Microbiol. 2012 Apr 11;10(5):323-35
pubmed: 22491358
Nat Commun. 2013;4:2151
pubmed: 23877117
BMC Bioinformatics. 2003 Sep 11;4:41
pubmed: 12969510
PLoS One. 2008 Feb 06;3(2):e1542
pubmed: 18253490
Gigascience. 2012 Dec 27;1(1):18
pubmed: 23587118
BMC Bioinformatics. 2013 Aug 15;14:248
pubmed: 23945046
Nat Methods. 2013 Sep;10(9):881-4
pubmed: 23892899
Nature. 2016 May 04;533(7604):543-546
pubmed: 27144353
Appl Environ Microbiol. 2009 Dec;75(23):7537-41
pubmed: 19801464
Cell Syst. 2016 Dec 21;3(6):572-584.e3
pubmed: 27818083
mBio. 2014 Apr 22;5(2):e00889
pubmed: 24757212
Nature. 2012 Jun 13;486(7402):215-21
pubmed: 22699610
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
Bioinformatics. 2009 Aug 1;25(15):1966-7
pubmed: 19497933
Nat Methods. 2013 Dec;10(12):1196-9
pubmed: 24141494
ISME J. 2015 Sep;9(9):1979-90
pubmed: 25647347
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W448-53
pubmed: 23677608
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W451-4
pubmed: 15980510
ISME J. 2013 May;7(5):949-61
pubmed: 23235287
Nat Rev Microbiol. 2014 Sep;12(9):635-45
pubmed: 25118885
Sci Rep. 2016 Apr 13;6:24373
pubmed: 27071527
Science. 2010 May 21;328(5981):994-9
pubmed: 20489017
Mol Microbiol. 2008 Jan;67(1):129-42
pubmed: 18047569
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D325-8
pubmed: 15608208
Nature. 2012 Oct 4;490(7418):55-60
pubmed: 23023125
Nat Rev Microbiol. 2016 Aug;14(8):508-22
pubmed: 27396567
Genome Res. 2003 Sep;13(9):2178-89
pubmed: 12952885
PLoS One. 2011;6(6):e21644
pubmed: 21738748
Nucleic Acids Res. 2009 Jan;37(Database issue):D443-7
pubmed: 18832362
Genome Res. 2015 Jul;25(7):1043-55
pubmed: 25977477
J Bacteriol. 2014 Jun;196(12):2210-5
pubmed: 24706738
Bioinformatics. 2009 Aug 1;25(15):1972-3
pubmed: 19505945
Nucleic Acids Res. 2016 Jan 4;44(D1):D694-7
pubmed: 26578559
Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4666-71
pubmed: 20855611
Nat Biotechnol. 2014 Aug;32(8):822-8
pubmed: 24997787
Nat Biotechnol. 2014 Aug;32(8):834-41
pubmed: 24997786
Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19126-31
pubmed: 19855009
Nat Rev Gastroenterol Hepatol. 2016 Feb;13(2):69-70
pubmed: 26828918
FEMS Microbiol Lett. 2009 May;294(1):1-8
pubmed: 19222573
Nucleic Acids Res. 2000 Jan 1;28(1):27-30
pubmed: 10592173
Cell. 2015 Feb 12;160(4):583-594
pubmed: 25640238
Proc Natl Acad Sci U S A. 2016 Jun 28;113(26):E3801-9
pubmed: 27286824
Int J Med Microbiol. 2002 Mar;291(8):605-14
pubmed: 12008914
BMC Bioinformatics. 2011 May 15;12:159
pubmed: 21575167
Science. 2017 Sep 15;357(6356):1156-1160
pubmed: 28912244
Nature. 2013 Jun 6;498(7452):99-103
pubmed: 23719380
Nucleic Acids Res. 2007;35(9):3100-8
pubmed: 17452365
Curr Opin Microbiol. 2010 Apr;13(2):232-9
pubmed: 20138000
Curr Opin Genet Dev. 2005 Dec;15(6):589-94
pubmed: 16185861
N Engl J Med. 2016 Dec 15;375(24):2369-2379
pubmed: 27974040
Nature. 2013 Jan 3;493(7430):45-50
pubmed: 23222524