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Literature DB >> 23892899

Accurate and universal delineation of prokaryotic species.

Daniel R Mende¹, Shinichi Sunagawa, Georg Zeller, Peer Bork.

Abstract

The exponentially increasing number of sequenced genomes necessitates fast, accurate, universally applicable and automated approaches for the delineation of prokaryotic species. We developed specI (species identification tool; http://www.bork.embl.de/software/specI/), a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes. Applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters. Of 314 discrepancies with a widely used taxonomic classification, >62% were resolved by literature support.

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Substances：

Year: 2013 PMID： 23892899 DOI： 10.1038/nmeth.2575

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

30 in total

1. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology.

Authors: Erko Stackebrandt; Wilhelm Frederiksen; George M Garrity; Patrick A D Grimont; Peter Kämpfer; Martin C J Maiden; Xavier Nesme; Ramon Rosselló-Mora; Jean Swings; Hans G Trüper; Luc Vauterin; Alan C Ward; William B Whitman
Journal: Int J Syst Evol Microbiol Date: 2002-05 Impact factor: 2.747

2. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2.

Authors: Martin Wu; Alexandra J Scott
Journal: Bioinformatics Date: 2012-02-12 Impact factor: 6.937

3. Quantitative phylogenetic assessment of microbial communities in diverse environments.

Authors: C von Mering; P Hugenholtz; J Raes; S G Tringe; T Doerks; L J Jensen; N Ward; P Bork
Journal: Science Date: 2007-02-01 Impact factor: 47.728

4. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.

Authors: Alexandros Stamatakis
Journal: Bioinformatics Date: 2006-08-23 Impact factor: 6.937

5. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes.

Authors: L R Moore; G Rocap; S W Chisholm
Journal: Nature Date: 1998-06-04 Impact factor: 49.962

6. Improved tools for biological sequence comparison.

Authors: W R Pearson; D J Lipman
Journal: Proc Natl Acad Sci U S A Date: 1988-04 Impact factor: 11.205

7. Fine-scale cospeciation between Brachycaudus and Buchnera aphidicola: bacterial genome helps define species and evolutionary relationships in aphids.

Authors: Emmanuelle Jousselin; Yves Desdevises; Armelle Coeur d'acier
Journal: Proc Biol Sci Date: 2009-01-07 Impact factor: 5.349

8. Concordant evolution of a symbiont with its host insect species: molecular phylogeny of genus Glossina and its bacteriome-associated endosymbiont, Wigglesworthia glossinidia.

Authors: X Chen; S Li; S Aksoy
Journal: J Mol Evol Date: 1999-01 Impact factor: 2.395

9. Identification of ribosomal RNA genes in metagenomic fragments.

Authors: Ying Huang; Paul Gilna; Weizhong Li
Journal: Bioinformatics Date: 2009-04-03 Impact factor: 6.937

10. eggNOG: automated construction and annotation of orthologous groups of genes.

Authors: Lars Juhl Jensen; Philippe Julien; Michael Kuhn; Christian von Mering; Jean Muller; Tobias Doerks; Peer Bork
Journal: Nucleic Acids Res Date: 2007-10-16 Impact factor: 16.971

153 in total

1. A null model for microbial diversification.

Authors: Timothy J Straub; Olga Zhaxybayeva
Journal: Proc Natl Acad Sci U S A Date: 2017-06-19 Impact factor: 11.205

2. Metagenomic species profiling using universal phylogenetic marker genes.

Authors: Shinichi Sunagawa; Daniel R Mende; Georg Zeller; Fernando Izquierdo-Carrasco; Simon A Berger; Jens Roat Kultima; Luis Pedro Coelho; Manimozhiyan Arumugam; Julien Tap; Henrik Bjørn Nielsen; Simon Rasmussen; Søren Brunak; Oluf Pedersen; Francisco Guarner; Willem M de Vos; Jun Wang; Junhua Li; Joël Doré; S Dusko Ehrlich; Alexandros Stamatakis; Peer Bork
Journal: Nat Methods Date: 2013-10-20 Impact factor: 28.547

10. Characterization and Recognition of Brachyspira hampsonii sp. nov., a Novel Intestinal Spirochete That Is Pathogenic to Pigs.

Authors: Nandita S Mirajkar; Nyree D Phillips; Tom La; David J Hampson; Connie J Gebhart
Journal: J Clin Microbiol Date: 2016-09-14 Impact factor: 5.948

Accurate and universal delineation of prokaryotic species.

1. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology.

2. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2.

3. Quantitative phylogenetic assessment of microbial communities in diverse environments.

4. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.

5. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes.

6. Improved tools for biological sequence comparison.

7. Fine-scale cospeciation between Brachycaudus and Buchnera aphidicola: bacterial genome helps define species and evolutionary relationships in aphids.

8. Concordant evolution of a symbiont with its host insect species: molecular phylogeny of genus Glossina and its bacteriome-associated endosymbiont, Wigglesworthia glossinidia.

9. Identification of ribosomal RNA genes in metagenomic fragments.

10. eggNOG: automated construction and annotation of orthologous groups of genes.

1. A null model for microbial diversification.

2. Metagenomic species profiling using universal phylogenetic marker genes.

3. Microbial species delineation using whole genome sequences.

4. Evaluating techniques for metagenome annotation using simulated sequence data.

5. Metabolic dependencies drive species co-occurrence in diverse microbial communities.

6. TIPP: taxonomic identification and phylogenetic profiling.

7. Aerococcus urinae Isolated from Women with Lower Urinary Tract Symptoms: In Vitro Aggregation and Genome Analysis.

8. Phylogeny of a relapsing fever Borrelia species transmitted by the hard tick Ixodes scapularis.

Review 9. Toward Accurate and Quantitative Comparative Metagenomics.

10. Characterization and Recognition of Brachyspira hampsonii sp. nov., a Novel Intestinal Spirochete That Is Pathogenic to Pigs.