Metagenomic species profiling using universal phylogenetic marker genes
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,
Dore J,
Ehrlich SD,
Stamatakis A,
Bork P,
Nat Methods
10
(12)
:1196-9
(2013).
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/.