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/.
authors.affiliation: European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Shinichi
authors.initials: S
authors.lastname: Sunagawa
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Mende
authors.forename: Georg
authors.initials: G
authors.lastname: Zeller
authors.forename: Fernando
authors.initials: F
authors.lastname: Izquierdo-Carrasco
authors.forename: Simon A
authors.initials: SA
authors.lastname: Berger
authors.forename: Jens Roat
authors.initials: JR
authors.lastname: Kultima
authors.forename: Luis Pedro
authors.initials: LP
authors.lastname: Coelho
authors.forename: Manimozhiyan
authors.identifier: 0000000208869101
authors.initials: M
authors.lastname: Arumugam
authors.forename: Julien
authors.initials: J
authors.lastname: Tap
authors.forename: Henrik Bjørn
authors.initials: HB
authors.lastname: Nielsen
authors.forename: Simon
authors.initials: S
authors.lastname: Rasmussen
authors.forename: Søren
authors.initials: S
authors.lastname: Brunak
authors.forename: Oluf
authors.initials: O
authors.lastname: Pedersen
authors.forename: Francisco
authors.initials: F
authors.lastname: Guarner
authors.forename: Willem M
authors.initials: WM
authors.lastname: de Vos
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Junhua
authors.initials: J
authors.lastname: Li
authors.forename: Joël
authors.initials: J
authors.lastname: Doré
authors.forename: S Dusko
authors.initials: SD
authors.lastname: Ehrlich
authors.forename: Alexandros
authors.initials: A
authors.lastname: Stamatakis
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D000465:Algorithms; D002138:Calibration; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D004275:DNA, Ribosomal / Q000235:genetics; D008040:Genetic Linkage; D005819:Genetic Markers; D016678:Genome; D006801:Humans; D007422:Intestines / Q000382:microbiology; D056186:Metagenomics; D064307:Microbiota; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D004275:DNA, Ribosomal; D005819:Genetic Markers; D012336:RNA, Ribosomal, 16S