title: Phylogenetic classification of short environmental DNA fragments.
abstract: Metagenomics is providing striking insights into the ecology of microbial communities. The recently developed massively parallel 454 pyrosequencing technique gives the opportunity to rapidly obtain metagenomic sequences at a low cost and without cloning bias. However, the phylogenetic analysis of the short reads produced represents a significant computational challenge. The phylogenetic algorithm CARMA for predicting the source organisms of environmental 454 reads is described. The algorithm searches for conserved Pfam domain and protein families in the unassembled reads of a sample. These gene fragments (environmental gene tags, EGTs), are classified into a higher-order taxonomy based on the reconstruction of a phylogenetic tree of each matching Pfam family. The method exhibits high accuracy for a wide range of taxonomic groups, and EGTs as short as 27 amino acids can be phylogenetically classified up to the rank of genus. The algorithm was applied in a comparative study of three aquatic microbial samples obtained by 454 pyrosequencing. Profound differences in the taxonomic composition of these samples could be clearly revealed.
authors.affiliation: Center for Biotechnology (CeBiTec), Bioinformatics Resource Facility (BRF), Bielefeld University, D-33594 Bielefeld, Germany. lutz.krause@cebitec.uni-bielefeld.de
authors.forename: Lutz
authors.initials: L
authors.lastname: Krause
authors.forename: Naryttza N
authors.initials: NN
authors.lastname: Diaz
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.forename: Scott
authors.initials: S
authors.lastname: Kelley
authors.forename: Tim W
authors.initials: TW
authors.lastname: Nattkemper
authors.forename: Forest
authors.initials: F
authors.lastname: Rohwer
authors.forename: Robert A
authors.initials: RA
authors.lastname: Edwards
authors.forename: Jens
authors.initials: J
authors.lastname: Stoye
mesh_terms: D000465:Algorithms; D004247:DNA / Q000145:classification; D004783:Environmental Microbiology; D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000145:classification; D012984:Software; D014871:Water Microbiology
chemical_list: D012336:RNA, Ribosomal, 16S; D004247:DNA