Accurate and universal delineation of prokaryotic species

By Daniel R. Mende, Shinichi Sunagawa, Georg Zeller, Peer Bork. 2013

329 citations recorded by the source corpus.

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Citations in the corpus

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2018, methodology): “In order to select best representative prokaryotic genomes, we used the SpecI species delineation method (18) against a total set of 25 038 genomes retrieved from RefSeq (19), obtaining 4445 reference species.”
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics (2016, background): “Unique clade-specific marker genes (Mende et al., 2013) and lowest common ancestor (LCA) positioning approaches are among the most popular.”
Microbial species delineation using whole genome sequences (2015, methodology): “Several reports have already illustrated that microbial taxonomic assignments are inconsistent with genetic information for a large number of species (17,29,30).”
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper (2016, methodology): “…species (TaxIDs 435591, 515620, 470145, 457412, 657321, 445970, 657317, 585543, 537011, and 43559) with a sequenced genome in the set of representative species defined by Mende et al. (2013) were used for simulation using a previously published metagenomics simulation tool (Mende et al. 2012).”
eggNOG v4.0: nested orthology inference across 3686 organisms (2013, methodology): “Theprokaryotic genomes were selected (29) from the RefSeq (34) repository.”
Structure and function of the global ocean microbiome (2015, methodology): “5 M gene-coding sequences and clustered them into metagenomic operational taxonomic units (mOTUs) that group organisms into species-level clusters at higher accuracy than 16S OTUs as described in (13, 24).”
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes (2016, methodology): “The MGs have been used to reconstruct the tree of life (17) and to study the phylogenetic relations within specific clades (13,20).”
Probiotics, gut microbiota, and their influence on host health and disease (2017, methodology): “In turn, phylogenetic analysis is supported by tools such as the CVTree server, which implements a whole genome-based, alignment-free composition vector method [118]; MetaPhlAn, which estimates the abundance of species in each sample according to the number of mapped reads to its markers [119]; and,”