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PMID: 24141494 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Metagenomic species profiling using universal phylogenetic marker genes.

Nature methods ·Vol. 10 ·No. 12 ·2013-12-00 ·Pages 1196-9

Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P

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/.

MeSH Terms
Algorithms Calibration Cluster Analysis Computational Biology/methods DNA, Ribosomal/genetics Genetic Linkage Genetic Markers Genome Humans Intestines/microbiology Metagenomics Microbiota Phylogeny RNA, Ribosomal, 16S/genetics Sequence Alignment/methods Sequence Analysis, DNA/methods
Chemicals
DNA, Ribosomal Genetic Markers RNA, Ribosomal, 16S
Authors & Affiliations
21 authors, click to expand affiliations / ORCID
Sunagawa Shinichi
European Molecular Biology Laboratory, Heidelberg, Germany.
Mende Daniel R
Zeller Georg
Izquierdo-Carrasco Fernando
Berger Simon A
Kultima Jens Roat
Coelho Luis Pedro
Arumugam Manimozhiyan ORCID
Tap Julien
Nielsen Henrik Bjørn
Rasmussen Simon
Brunak Søren
Pedersen Oluf
Guarner Francisco
de Vos Willem M
Wang Jun
Li Junhua
Doré Joël
Ehrlich S Dusko
Stamatakis Alexandros
Bork Peer
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Article Info
Journal
Nature methods
Abbr.
Nat Methods
ISSN
1548-7105
DOI
10.1038/nmeth.2693
Published
2013-12-00
Epub
2013-00-20
Pages
1196-9
Language
English
Region
United States
NLM ID
101215604
Subset
IM
External Links
PubMed source DOI: 10.1038/nmeth.2693 View journal details
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