Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

被引：869

作者：

Nielsen, H. Bjorn ^{[1
,2
]}

Almeida, Mathieu ^{[3
,4
,5
]}

Juncker, Agnieszka Sierakowska ^{[1
,2
]}

Rasmussen, Simon ^{[1
]}

Li, Junhua ^{[6
,7
,8
]}

Sunagawa, Shinichi ^{[9
]}

Plichta, Damian R. ^{[1
]}

Gautier, Laurent ^{[1
]}

Pedersen, Anders G. ^{[1
]}

Le Chatelier, Emmanuelle ^{[3
,4
]}

Pelletier, Eric ^{[10
,11
,12
]}

Bonde, Ida ^{[1
,2
]}

Nielsen, Trine ^{[13
]}

Manichanh, Chaysavanh ^{[14
]}

Arumugam, Manimozhiyan ^{[7
,13
]}

Batto, Jean-Michel ^{[3
,4
]}

dos Santos, Marcelo B. Quintanilha ^{[1
]}

Blom, Nikolaj ^{[2
]}

Borruel, Natalia ^{[14
]}

Burgdorf, Kristoffer S. ^{[13
]}

Boumezbeur, Fouad ^{[4
]}

Casellas, Francesc ^{[14
]}

Dore, Joel ^{[3
,4
]}

Dworzynski, Piotr ^{[1
]}

Guarner, Francisco ^{[14
]}

Hansen, Torben ^{[13
,15
]}

Hildebrand, Falk ^{[16
,17
]}

Kaas, Rolf S. ^{[18
]}

Kennedy, Sean ^{[3
,4
]}

Kristiansen, Karsten ^{[19
]}

Kultima, Jens Roat ^{[9
]}

Leonard, Pierre ^{[4
]}

Levenez, Florence ^{[3
,4
]}

Lund, Ole ^{[1
]}

Moumen, Bouziane ^{[3
,4
]}

Le Paslier, Denis ^{[10
,11
,12
]}

Pons, Nicolas ^{[3
,4
]}

Pedersen, Oluf ^{[13
,20
,21
,22
]}

Prifti, Edi ^{[3
,4
]}

Qin, Junjie ^{[6
,7
]}

Raes, Jeroen ^{[17
,23
,24
]}

Sorensen, Soren ^{[25
]}

Tap, Julien ^{[9
]}

Tims, Sebastian ^{[26
]}

Ussery, David W. ^{[1
]}

Yamada, Takuji ^{[9
,27
]}

Renault, Pierre ^{[3
]}

Sicheritz-Ponten, Thomas ^{[1
,2
]}

Bork, Peer ^{[9
,28
]}

Wang, Jun ^{[7
,13
,19
,29
]}

机构：

[1] Tech Univ Denmark, Ctr Biol Sequence Anal, Kongens Lyngby, Denmark

[2] Tech Univ Denmark, Novo Nordisk Fdn Ctr Biosustainabil, Kongens Lyngby, Denmark

[3] INRA, UMR 14121 MICALIS, Jouy En Josas, France

[4] INRA, US 1367 Metagenopolis, Jouy En Josas, France

[5] Univ Maryland, Ctr Bioinformat & Computat Biol, Dept Comp Sci, College Pk, MD USA

[6] BGI Hong Kong Res Inst, Hong Kong, Hong Kong, Peoples R China

[7] BGI Shenzhen, Shenzhen, Peoples R China

[8] S China Univ Technol, Sch Biosci & Biotechnol, Guangzhou, Guangdong, Peoples R China

[9] European Mol Biol Lab, D-69012 Heidelberg, Germany

[10] Inst Genom, Commissariat Energie Atom & Energies Alternat, Evry, France

[11] Ctr Natl Rech Scientif, Evry, France

[12] Univ Evry Val dEssonne, Evry, France

[13] Univ Copenhagen, Novo Nordisk Fdn Ctr Basic Metabol Res, Copenhagen, Denmark

[14] Univ Hosp Vall dHebron, Digest Syst Res Unit, Ciberehd, Barcelona, Spain

[15] Univ So Denmark, Fac Hlth Sci, Odense, Denmark

[16] VIB, Dept Biol Struct, Brussels, Belgium

[17] Vrije Univ Brussel, Dept Biosci Engn, Brussels, Belgium

[18] Tech Univ Denmark, Natl Food Inst, Div Epidemiol & Microbial Gen, Kongens Lyngby, Denmark

[19] Univ Copenhagen, Dept Biol, Copenhagen, Denmark

[20] Hagedorn Res Inst, Gentofte, Denmark

[21] Univ Copenhagen, Fac Hlth & Med Sci, Inst Biomed Sci, Copenhagen, Denmark

[22] Aarhus Univ, Fac Hlth, Aarhus, Denmark

[23] Katholieke Univ Leuven, Rega Inst, Dept Microbiol & Immunol, Louvain, Belgium

[24] VIB, Ctr Biol Dis, Leuven, Belgium

[25] Univ Copenhagen, Dept Biol, Microbiol Sect, Copenhagen, Denmark

[26] Wageningen Univ, Microbiol Lab, NL-6700 AP Wageningen, Netherlands

[27] Tokyo Inst Technol, Dept Biol Informat, Yokohama, Kanagawa 227, Japan

[28] Max Delbruck Ctr Mol Med, Berlin, Germany

[29] King Abdulaziz Univ, Princess Al Jawhara Ctr Excellence Res Hereditary, Jeddah 21413, Saudi Arabia

[30] Kings Coll London, Guys Hosp, Ctr Host Microbiome Interact, Dent Inst Cent Off, London WC2R 2LS, England

来源：

NATURE BIOTECHNOLOGY | 2014年 / 32卷 / 08期

关键词：

MICROBIOTA; SEQUENCE; TREE; SETS; TOOL;

D O I：

10.1038/nbt.2939

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 [微生物学]; 090105 [作物生产系统与生态工程];

摘要：

Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases. De novo segregation of complex metagenomic data into specific biological entities, such as particular bacterial strains or viruses, remains a largely unsolved problem. Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences. We demonstrate the method on data from 396 human gut microbiome samples and identify 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS). We use these to assemble 238 high-quality microbial genomes and identify affiliations between MGS and hundreds of viruses or genetic entities. Our method provides the means for comprehensive profiling of the diversity within complex metagenomic samples.

引用

页码：822 / 828

页数：7

共 50 条

[41]

Application of tetranucleotide frequencies for the assignment of genomic fragments [J].

Teeling, H ;

Meyerdierks, A ;

Bauer, M ;

Amann, R ;

Glöckner, FO .

ENVIRONMENTAL MICROBIOLOGY, 2004, 6 (09) :938-947

[42]

CRISPR-based adaptive immune systems [J].

Terns, Michael P. ;

Terns, Rebecca M. .

CURRENT OPINION IN MICROBIOLOGY, 2011, 14 (03) :321-327

[43]

Treangen Todd J, 2011, Curr Protoc Bioinformatics, VChapter 11, DOI 10.1002/0471250953.bi1108s33

[44]

Comparative metagenomics of microbial communities [J].

Tringe, SG ;

von Mering, C ;

Kobayashi, A ;

Salamov, AA ;

Chen, K ;

Chang, HW ;

Podar, M ;

Short, JM ;

Mathur, EJ ;

Detter, JC ;

Bork, P ;

Hugenholtz, P ;

Rubin, EM .

SCIENCE, 2005, 308 (5721) :554-557

[45]

MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample [J].

Wang, Yi ;

Leung, Henry C. M. ;

Yiu, S. M. ;

Chin, Francis Y. L. .

BIOINFORMATICS, 2012, 28 (18) :I356-I362

[46]

A Primer on Metagenomics [J].

Wooley, John C. ;

Godzik, Adam ;

Friedberg, Iddo .

PLOS COMPUTATIONAL BIOLOGY, 2010, 6 (02)

[47]

Identification of acquired antimicrobial resistance genes [J].

Zankari, Ea ;

Hasman, Henrik ;

Cosentino, Salvatore ;

Vestergaard, Martin ;

Rasmussen, Simon ;

Lund, Ole ;

Aarestrup, Frank M. ;

Larsen, Mette Voldby .

JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 2012, 67 (11) :2640-2644

[48]

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs [J].

Zerbino, Daniel R. ;

Birney, Ewan .

GENOME RESEARCH, 2008, 18 (05) :821-829

[49]

CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes [J].

Zhang, Quan ;

Rho, Mina ;

Tang, Haixu ;

Doak, Thomas G. ;

Ye, Yuzhen .

GENOME BIOLOGY, 2013, 14 (04)

[50]

Ab initio gene identification in metagenomic sequences [J].

Zhu, Wenhan ;

Lomsadze, Alexandre ;

Borodovsky, Mark .

NUCLEIC ACIDS RESEARCH, 2010, 38 (12) :e132

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