Metagenomic species profiling using universal phylogenetic marker genes

Shinichi Sunagawa; Daniel R. Mende; Georg Zeller; Fernando Izquierdo-Carrasco; Simon A. Berger; Jens Roat Kultima; Luis Pedro Coelho; Manimozhiyan Arumugam; Julien Tap; Henrik Bjørn Nielsen; Simon Rasmussen; Søren Brunak; Oluf Borbye Pedersen; Francisco Guarner; Willem M de Vos; Jun Wang; Junhua Li; Joël Doré; S Dusko Ehrlich; Alexandros Stamatakis; Peer Bork

doi:10.1038/nmeth.2693

Metagenomic species profiling using universal phylogenetic marker genes

Shinichi Sunagawa, Daniel R. Mende, Georg Zeller, Fernando Izquierdo-Carrasco, Simon A. Berger, Jens Roat Kultima, Luis Pedro Coelho, Manimozhiyan Arumugam, Julien Tap, Henrik Bjørn Nielsen, Simon Rasmussen, Søren Brunak, Oluf Borbye Pedersen, Francisco Guarner, Willem M de Vos, Jun Wang, Junhua Li, Joël Doré, S Dusko Ehrlich, Alexandros StamatakisPeer Bork

Genomforskning og Molekylær Biomedicin

253 Citationer (Scopus)

Abstract

To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/.

Originalsprog	Engelsk
Tidsskrift	Nature Methods
Vol/bind	10
Udgave nummer	12
Sider (fra-til)	1196-1199
Antal sider	4
ISSN	1548-7091
DOI	https://doi.org/10.1038/nmeth.2693
Status	Udgivet - dec. 2013

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10.1038/nmeth.2693

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Sunagawa, S., Mende, D. R., Zeller, G., Izquierdo-Carrasco, F., Berger, S. A., Kultima, J. R., Coelho, L. P., Arumugam, M., Tap, J., Nielsen, H. B., Rasmussen, S., Brunak, S., Pedersen, O. B., Guarner, F., de Vos, W. M., Wang, J., Li, J., Doré, J., Ehrlich, S. D., ... Bork, P. (2013). Metagenomic species profiling using universal phylogenetic marker genes. Nature Methods, 10(12), 1196-1199. https://doi.org/10.1038/nmeth.2693

Sunagawa, S, Mende, DR, Zeller, G, Izquierdo-Carrasco, F, Berger, SA, Kultima, JR, Coelho, LP, Arumugam, M, Tap, J, Nielsen, HB, Rasmussen, S, Brunak, S, Pedersen, OB, Guarner, F, de Vos, WM, Wang, J, Li, J, Doré, J, Ehrlich, SD, Stamatakis, A & Bork, P 2013, 'Metagenomic species profiling using universal phylogenetic marker genes', Nature Methods, bind 10, nr. 12, s. 1196-1199. https://doi.org/10.1038/nmeth.2693

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title = "Metagenomic species profiling using universal phylogenetic marker genes",

abstract = "To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/.",

author = "Shinichi Sunagawa and Mende, {Daniel R.} and Georg Zeller and Fernando Izquierdo-Carrasco and Berger, {Simon A.} and Kultima, {Jens Roat} and Coelho, {Luis Pedro} and Manimozhiyan Arumugam and Julien Tap and Nielsen, {Henrik Bj{\o}rn} and Simon Rasmussen and S{\o}ren Brunak and Pedersen, {Oluf Borbye} and Francisco Guarner and {de Vos}, {Willem M} and Jun Wang and Junhua Li and Jo{\"e}l Dor{\'e} and Ehrlich, {S Dusko} and Alexandros Stamatakis and Peer Bork",

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month = dec,

doi = "10.1038/nmeth.2693",

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T1 - Metagenomic species profiling using universal phylogenetic marker genes

AU - Sunagawa, Shinichi

AU - Mende, Daniel R.

AU - Zeller, Georg

AU - Izquierdo-Carrasco, Fernando

AU - Berger, Simon A.

AU - Kultima, Jens Roat

AU - Coelho, Luis Pedro

AU - Arumugam, Manimozhiyan

AU - Tap, Julien

AU - Nielsen, Henrik Bjørn

AU - Rasmussen, Simon

AU - Brunak, Søren

AU - Pedersen, Oluf Borbye

AU - Guarner, Francisco

AU - de Vos, Willem M

AU - Wang, Jun

AU - Li, Junhua

AU - Doré, Joël

AU - Ehrlich, S Dusko

AU - Stamatakis, Alexandros

AU - Bork, Peer

PY - 2013/12

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N2 - To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/.

AB - To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/.

U2 - 10.1038/nmeth.2693

DO - 10.1038/nmeth.2693

M3 - Journal article

C2 - 24141494

SN - 1548-7091

VL - 10

SP - 1196

EP - 1199

JO - Nature Methods

JF - Nature Methods

IS - 12

ER -

Metagenomic species profiling using universal phylogenetic marker genes

Abstract

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