Metagenomic Species Profiling Using Universal Phylogenetic Marker Genes

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2013 Oct 22

PMID 24141494

Citations 269

Authors

Shinichi Sunagawa

Daniel R Mende

Georg Zeller

Fernando Izquierdo-Carrasco

Simon A Berger

Jens Roat Kultima

Luis Pedro Coelho

Manimozhiyan Arumugam

Julien Tap

Henrik Bjorn Nielsen

Simon Rasmussen

Soren Brunak

Oluf Pedersen

Francisco Guarner

Willem M de Vos

Jun Wang

Junhua Li

Joel Dore

S Dusko Ehrlich

Alexandros Stamatakis

Peer Bork

Affiliations

Soon will be listed here.

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/.

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