Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
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Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. / Nielsen, H Bjørn; Almeida, Mathieu; Juncker, Agnieszka; Rasmussen, Simon; Li, Junhua; Sunagawa, Shinichi; Plichta, Damian Rafal; Gautier, Laurent; Pedersen, Anders G.; Le Chatelier, Emmanuelle; Pelletier, Eric; Bonde, Ida; Nielsen, Trine; Manichanh, Chaysavanh; Arumugam, Manimozhiyan; Batto, Jean-Michel; dos Santos, Marcelo Bertalan Quintanilha; Blom, Nikolaj; Borruel, Natalia; Burgdorf, Kristoffer Sølvsten; Boumezbeur, Fouad; Casellas, Francesc; Doré, Joël; Dworzynski, Piotr; Guarner, Francisco; Hansen, Torben; Hildebrand, Falk; Kaas, Rolf Sommer; Kennedy, Sean; Kristiansen, Karsten; Kultima, Jens Roat; Léonard, Pierre; Levenez, Florence; Lund, Ole; Moumen, Bouziane; Le Paslier, Denis; Pons, Nicolas; Pedersen, Oluf Borbye; Prifti, Edi; Qin, Junjie; Raes, Jeroen; Sørensen, Søren Johannes; Tap, Julien; Tims, Sebastian; Ussery, David; Yamada, Takuji; Renault, Pierre; Sicheritz-Pontén, Thomas; Bork, Peer; Wang, Jun; MetaHIT Consortium.
In: Nature Biotechnology, Vol. 32, No. 8, 2014, p. 822–828.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
AU - Nielsen, H Bjørn
AU - Almeida, Mathieu
AU - Juncker, Agnieszka
AU - Rasmussen, Simon
AU - Li, Junhua
AU - Sunagawa, Shinichi
AU - Plichta, Damian Rafal
AU - Gautier, Laurent
AU - Pedersen, Anders G.
AU - Le Chatelier, Emmanuelle
AU - Pelletier, Eric
AU - Bonde, Ida
AU - Nielsen, Trine
AU - Manichanh, Chaysavanh
AU - Arumugam, Manimozhiyan
AU - Batto, Jean-Michel
AU - dos Santos, Marcelo Bertalan Quintanilha
AU - Blom, Nikolaj
AU - Borruel, Natalia
AU - Burgdorf, Kristoffer Sølvsten
AU - Boumezbeur, Fouad
AU - Casellas, Francesc
AU - Doré, Joël
AU - Dworzynski, Piotr
AU - Guarner, Francisco
AU - Hansen, Torben
AU - Hildebrand, Falk
AU - Kaas, Rolf Sommer
AU - Kennedy, Sean
AU - Kristiansen, Karsten
AU - Kultima, Jens Roat
AU - Léonard, Pierre
AU - Levenez, Florence
AU - Lund, Ole
AU - Moumen, Bouziane
AU - Le Paslier, Denis
AU - Pons, Nicolas
AU - Pedersen, Oluf Borbye
AU - Prifti, Edi
AU - Qin, Junjie
AU - Raes, Jeroen
AU - Sørensen, Søren Johannes
AU - Tap, Julien
AU - Tims, Sebastian
AU - Ussery, David
AU - Yamada, Takuji
AU - Renault, Pierre
AU - Sicheritz-Pontén, Thomas
AU - Bork, Peer
AU - Wang, Jun
AU - MetaHIT Consortium
PY - 2014
Y1 - 2014
N2 - 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.
AB - 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.
U2 - 10.1038/nbt.2939
DO - 10.1038/nbt.2939
M3 - Journal article
C2 - 24997787
VL - 32
SP - 822
EP - 828
JO - Nature Biotechnology
JF - Nature Biotechnology
SN - 1087-0156
IS - 8
ER -
ID: 119293516