Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.
Animals
Cattle
Clustered Regularly Interspaced Short Palindromic Repeats
Drug Resistance, Microbial
/ genetics
Gene Transfer, Horizontal
Genes, Microbial
Metagenomics
/ methods
Microbiota
/ genetics
Open Reading Frames
Prophages
/ genetics
Rumen
/ microbiology
Sequence Analysis, DNA
/ methods
Viruses
/ genetics
Hi-C
Metagenome assembly
Metagenomics
PacBio
Virus-host association
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
02 08 2019
02 08 2019
Historique:
received:
08
12
2018
accepted:
02
07
2019
entrez:
4
8
2019
pubmed:
4
8
2019
medline:
28
10
2019
Statut:
epublish
Résumé
We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.
Identifiants
pubmed: 31375138
doi: 10.1186/s13059-019-1760-x
pii: 10.1186/s13059-019-1760-x
pmc: PMC6676630
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
153Subventions
Organisme : NIAID NIH HHS
ID : R43 AI122654
Pays : United States
Organisme : NIAID NIH HHS
ID : R44 AI122654
Pays : United States
Organisme : NIAID NIH HHS
ID : R44 AI150008
Pays : United States
Organisme : National Institute of Allergy and Infectious Diseases (US)
ID : R44AI122654-02A1
Pays : International
Références
Anaerobe. 2015 Oct;35(Pt B):3-10
pubmed: 26103451
Nat Microbiol. 2018 Jul;3(7):836-843
pubmed: 29807988
Front Microbiol. 2018 Apr 30;9:850
pubmed: 29760690
Nat Microbiol. 2018 Nov;3(11):1274-1284
pubmed: 30356154
Nat Methods. 2016 Sep;13(9):751-4
pubmed: 27454285
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Genome Res. 2017 May;27(5):824-834
pubmed: 28298430
mBio. 2016 Feb 09;7(1):e01948-15
pubmed: 26861018
BMC Bioinformatics. 2010 Mar 08;11:119
pubmed: 20211023
Microbiome. 2017 Nov 28;5(1):155
pubmed: 29179741
Front Microbiol. 2014 Dec 09;5:689
pubmed: 25538699
BMC Microbiol. 2016 Nov 14;16(1):274
pubmed: 27842515
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Nat Rev Genet. 2013 Mar;14(3):157-67
pubmed: 23358380
Bioinformatics. 2019 Jun 1;35(12):2150-2152
pubmed: 30418481
PLoS One. 2014 Feb 13;9(2):e88339
pubmed: 24551092
Sci Adv. 2017 Feb 17;3(2):e1602105
pubmed: 28232956
Microbiome. 2017 Dec 11;5(1):159
pubmed: 29228991
Sci Rep. 2018 Jan 16;8(1):814
pubmed: 29339831
Nat Methods. 2017 Nov;14(11):1063-1071
pubmed: 28967888
Biotechniques. 2004 May;36(5):808-12
pubmed: 15152600
Bioinformatics. 2015 May 15;31(10):1674-6
pubmed: 25609793
Science. 2011 Jan 28;331(6016):463-7
pubmed: 21273488
Gigascience. 2017 Mar 1;6(3):1-10
pubmed: 28327976
Sci Rep. 2017 Jan 18;7:40864
pubmed: 28098248
Nat Biotechnol. 2018 Apr;36(4):359-367
pubmed: 29553575
Sci Transl Med. 2014 Sep 17;6(254):254ra126
pubmed: 25232178
J Antimicrob Chemother. 2012 Nov;67(11):2640-4
pubmed: 22782487
Appl Environ Microbiol. 2001 Feb;67(2):561-8
pubmed: 11157217
Front Microbiol. 2015 Apr 10;6:296
pubmed: 25914693
G3 (Bethesda). 2014 May 22;4(7):1339-46
pubmed: 24855317
Appl Environ Microbiol. 2015 Jul;81(14):4697-710
pubmed: 25934629
Nat Commun. 2018 Feb 28;9(1):870
pubmed: 29491419
Bioinformatics. 2016 Jul 15;32(14):2103-10
pubmed: 27153593
Nucleic Acids Res. 1989 Feb 25;17(4):1327-35
pubmed: 2922283
Nature. 2008 Nov 6;456(7218):53-9
pubmed: 18987734
Science. 2016 Sep 16;353(6305):1272-7
pubmed: 27634532
Nucleic Acids Res. 2006;34(20):5839-51
pubmed: 17062630
Appl Microbiol Biotechnol. 2007 May;75(1):165-74
pubmed: 17235560
Sci Rep. 2016 May 09;6:25373
pubmed: 27156482
Genome Res. 2015 Jul;25(7):1043-55
pubmed: 25977477
Nat Methods. 2015 Aug;12(8):780-6
pubmed: 26121404
Nat Methods. 2015 Jan;12(1):59-60
pubmed: 25402007
Genome Res. 2017 May;27(5):787-792
pubmed: 28130360
Nat Genet. 2017 Apr;49(4):643-650
pubmed: 28263316
Genome Biol. 2016 Jun 20;17(1):132
pubmed: 27323842
Nat Biotechnol. 2017 Aug 8;35(8):725-731
pubmed: 28787424
Mol Biol Evol. 2017 Aug 1;34(8):2115-2122
pubmed: 28460117
PLoS One. 2013 Sep 11;8(9):e74787
pubmed: 24040342
Science. 2009 Jan 2;323(5910):133-8
pubmed: 19023044
PeerJ. 2015 Aug 27;3:e1165
pubmed: 26336640