Metagenomic species profiling using universal phylogenetic marker genes

Shinichi Sunagawa (1) , Daniel R. Mende (1) , Georg Zeller (1) , Fernando Izquierdo-Carrasco (2) , Simon A. Berger (2) , Jens Roat Kultima (1) , Luis Pedro Coelho (2) , Manimozhiyan Arumugam (3, 4, 1) , Julien Tap (5, 1) , Henrik Bjørn Nielsen (6) , Simon Rasmussen (7) , Soren Brunak (7) , Oluf Pedersen (4, 8, 9) , Francisco Guarner (10) , Willem M. de Vos (11, 12) , Jun Wang (13, 3, 4, 14) , Junhua Li (3, 3, 15) , Joel Dore (16, 5) , Stanislav Ehrlich (5) , Alexandros Stamatakis (17, 2) , Peer Bork (18, 1)

1 EMBL - European Molecular Biology Laboratory [Grenoble]
2 The Exelixis Lab, Scientific Computing Group
3 BGI - Beijing Genomics Institute [Shenzhen]
4 CBMR - Novo Nordisk Foundation Center for Basic Metabolic Research
5 MetaGenoPolis
6 Center for Biological Sequence Analysis - Novo Nordisk Foundation Center for Biosustainability
7 Center for Biological Sequence Analysis
8 Hagedorn Research Institute
9 Faculty of Health Sciences
10 Digestive System Research Unit
11 Laboratory of Microbiology
12 Department of Bacteriology and Immunology [Helsinki]
13 King Abdulaziz University
14 MUST - Macau University of Science and Technology
15 School of Bioscience and Biotechnology
16 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
17 Institute for Theoretical Informatics
18 MDC - Max Delbrück Center for Molecular Medicine [Berlin]

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/.

Domaines: Sciences du Vivant [q-bio]

Shinichi Sunagawa, Daniel R. Mende, Georg Zeller, Fernando Izquierdo-Carrasco, Simon A. Berger, et al.. Metagenomic species profiling using universal phylogenetic marker genes. Nature Methods, 2013, 10 (12), pp.1196 - +. ⟨10.1038/NMETH.2693⟩. ⟨hal-01204281⟩