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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
Nature Biotechnology, Volume 32, No. 8, Year 2014
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Description
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. © 2014 Nature America, Inc.
Authors & Co-Authors
Nielsen, H. Bjørn
Unknown Affiliation
Almeida, Mathieu
Unknown Affiliation
Juncker, Agnieszka S.
Unknown Affiliation
Rasmussen, S. B.
Unknown Affiliation
Li, Junhua
Unknown Affiliation
Sunagawa, Shinichi
Unknown Affiliation
Plichta, Damian R.
Unknown Affiliation
Gautier, Laurant
Unknown Affiliation
Pedersen, Anders Gorm
Unknown Affiliation
Chatelier, Emmanuelle Le
Unknown Affiliation
Pelletier, Éric
Unknown Affiliation
Bonde, Ida
Unknown Affiliation
Nielsen, Trine G.
Unknown Affiliation
Manichanh, Chaysavanh
Unknown Affiliation
Arumugam, Manimozhiyan
Unknown Affiliation
Batto, Jean Michel
Unknown Affiliation
Quintanilha Dos Santos, Marcelo B.
Unknown Affiliation
Blom, Nikolaj
Unknown Affiliation
Borruel, Natalia
Unknown Affiliation
Burgdorf, Kristoffer S.
Unknown Affiliation
Boumezbeur, Fouad
Unknown Affiliation
Casellas, Francesc
Unknown Affiliation
Doré, Joël
Unknown Affiliation
Dworzyński, Piotr
Unknown Affiliation
Guarner, Francisco
Unknown Affiliation
Hansen, Torben Frøstrup
Unknown Affiliation
Hildebrand, Falk
Unknown Affiliation
Kaas, Rolf Sommer
Unknown Affiliation
Kennedy, Sean P.
Unknown Affiliation
Kristiansen, Karsten
Unknown Affiliation
Kultima, Jens Roat
Unknown Affiliation
Leonard, Pierre
Unknown Affiliation
Levenez, Florence
Unknown Affiliation
Lund, Ole Sogaard
Unknown Affiliation
Moumen, Bouziane
Unknown Affiliation
Le Paslier, Denis L.
Unknown Affiliation
Pons, Nicolas
Unknown Affiliation
Pedersen, Oluf Borbye
Unknown Affiliation
Prifti, Edi
Unknown Affiliation
Qin, Junjie
Unknown Affiliation
Raes, Jeroen
Unknown Affiliation
Sørensen, Søren J.
Unknown Affiliation
Tap, Julien
Unknown Affiliation
Tims, Sebastian
Unknown Affiliation
Ussery, David Wayne
Unknown Affiliation
Yamada, Takuji
Unknown Affiliation
Renault, Pierre P.
Unknown Affiliation
Sicheritz-Pontén, Thomas E.
Unknown Affiliation
Bork, Peer
Unknown Affiliation
Wang, Jun
Unknown Affiliation
Brunak, Søren B.
Unknown Affiliation
Ehrlich, Stanislav Dusko
Unknown Affiliation
Jamet, Alexandre
Unknown Affiliation
Mérieux, Alexandre
Unknown Affiliation
Cultrone, Antonella
Unknown Affiliation
Torrejon, Antonio
Unknown Affiliation
Quinquis, Benoît
Unknown Affiliation
Bréchot, Christian B.
Unknown Affiliation
Delorme, Christine
Unknown Affiliation
M’rini, Christine
Unknown Affiliation
de Vos, Willem Meindert
Unknown Affiliation
Maguin, Emmanuelle
Unknown Affiliation
Varela, Encarna
Unknown Affiliation
Guedon, Eric
Unknown Affiliation
Gwen, Falony
Unknown Affiliation
Haimet, Florence
Unknown Affiliation
Artiguenave, François
Unknown Affiliation
Vandemeulebrouck, Gaetana
Unknown Affiliation
Denariaz, Gérard
Unknown Affiliation
Khaci, Ghalia
Unknown Affiliation
Blottière, Hervé M.
Unknown Affiliation
Knol, Jan
Unknown Affiliation
Weissenbach, Jean S.
Unknown Affiliation
van Hylckama Vlieg, Johan E.T.
Unknown Affiliation
Torben, Jørgensen
Unknown Affiliation
Parkhill, Julian
Unknown Affiliation
Turner, Keith
Unknown Affiliation
van de Guchte, Maarten
Unknown Affiliation
Antolin, Maria
Unknown Affiliation
Rescigno, Maria
Unknown Affiliation
Kleerebezem, Michiel
Unknown Affiliation
Derrien, Muriel
Unknown Affiliation
Galleron, Nathalie
Unknown Affiliation
Sanchez, Nicolas
Unknown Affiliation
Grarup, Niels
Unknown Affiliation
Veiga, Patrick
Unknown Affiliation
Oozeer, Raish
Unknown Affiliation
Dervyn, Rozenn
Unknown Affiliation
Layec, Séverine
Unknown Affiliation
Bruls, Thomas
Unknown Affiliation
Winogradski, Yohanan
Unknown Affiliation
Erwin, Zoetendal
Unknown Affiliation
Statistics
Citations: 877
Authors: 92
Affiliations: 33
Identifiers
Doi:
10.1038/nbt.2939
ISSN:
10870156
e-ISSN:
15461696
Research Areas
Genetics And Genomics
Infectious Diseases