Literature DB >> 17062410

Stepping stones towards a new prokaryotic taxonomy.

Dirk Gevers1, Peter Dawyndt, Peter Vandamme, Anne Willems, Marc Vancanneyt, Jean Swings, Paul De Vos.   

Abstract

Technological developments provide new insights into prokaryotic evolution and diversity and provoke a continuous need to update taxonomy and revise classification schemes. Our present species concept and definition are being challenged by the growing amount of whole genomic information, which should allow improvements in the natural species definition. The continuous quest for an objective and stable method for sorting strains into coherent homogeneous groups is inherent to prokaryotic systematics and nomenclature. Morphological, biochemical, physiological, phenotypic and chemotaxonomic criteria have been complemented by molecular data and pragmatic, purpose built, species definitions are being replaced by more natural ones based on evolutionary insights. It is imperative to give due consideration to both fundamental and applied aspects of future species concepts and definitions. The present paper discusses the present practice in prokaryotic taxonomy of how this system developed and how it may evolve in the future.

Mesh:

Year:  2006        PMID: 17062410      PMCID: PMC1764938          DOI: 10.1098/rstb.2006.1915

Source DB:  PubMed          Journal:  Philos Trans R Soc Lond B Biol Sci        ISSN: 0962-8436            Impact factor:   6.237


  21 in total

Review 1.  A natural species concept for prokaryotes.

Authors:  D M Ward
Journal:  Curr Opin Microbiol       Date:  1998-06       Impact factor: 7.934

2.  Does a tree-like phylogeny only exist at the tips in the prokaryotes?

Authors:  Christopher J Creevey; David A Fitzpatrick; Gayle K Philip; Rhoda J Kinsella; Mary J O'Connell; Melissa M Pentony; Simon A Travers; Mark Wilkinson; James O McInerney
Journal:  Proc Biol Sci       Date:  2004-12-22       Impact factor: 5.349

3.  Towards a genome-based taxonomy for prokaryotes.

Authors:  Konstantinos T Konstantinidis; James M Tiedje
Journal:  J Bacteriol       Date:  2005-09       Impact factor: 3.490

Review 4.  Opinion: Re-evaluating prokaryotic species.

Authors:  Dirk Gevers; Frederick M Cohan; Jeffrey G Lawrence; Brian G Spratt; Tom Coenye; Edward J Feil; Erko Stackebrandt; Yves Van de Peer; Peter Vandamme; Fabiano L Thompson; Jean Swings
Journal:  Nat Rev Microbiol       Date:  2005-09       Impact factor: 60.633

5.  The net of life: reconstructing the microbial phylogenetic network.

Authors:  Victor Kunin; Leon Goldovsky; Nikos Darzentas; Christos A Ouzounis
Journal:  Genome Res       Date:  2005-06-17       Impact factor: 9.043

Review 6.  Community genomics in microbial ecology and evolution.

Authors:  Eric E Allen; Jillian F Banfield
Journal:  Nat Rev Microbiol       Date:  2005-06       Impact factor: 60.633

7.  Towards a conceptual and operational union of bacterial systematics, ecology, and evolution.

Authors:  Frederick M Cohan
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2006-11-29       Impact factor: 6.237

Review 8.  The bacterial species definition in the genomic era.

Authors:  Konstantinos T Konstantinidis; Alban Ramette; James M Tiedje
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2006-11-29       Impact factor: 6.237

9.  Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the gamma-proteobacteria.

Authors:  E Susko; J Leigh; W F Doolittle; E Bapteste
Journal:  Mol Biol Evol       Date:  2006-02-22       Impact factor: 16.240

Review 10.  Sequences, sequence clusters and bacterial species.

Authors:  William P Hanage; Christophe Fraser; Brian G Spratt
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2006-11-29       Impact factor: 6.237

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  9 in total

Review 1.  Biased gene transfer in microbial evolution.

Authors:  Cheryl P Andam; J Peter Gogarten
Journal:  Nat Rev Microbiol       Date:  2011-06-13       Impact factor: 60.633

Review 2.  Population genetics, taxonomy, phylogeny and evolution of Borrelia burgdorferi sensu lato.

Authors:  Gabriele Margos; Stephanie A Vollmer; Nicholas H Ogden; Durland Fish
Journal:  Infect Genet Evol       Date:  2011-08-05       Impact factor: 3.342

3.  A new Borrelia species defined by multilocus sequence analysis of housekeeping genes.

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Journal:  Appl Environ Microbiol       Date:  2009-06-19       Impact factor: 4.792

4.  An In-depth Analysis of a Multilocus Phylogeny Identifies leuS As a Reliable Phylogenetic Marker for the Genus Pantoea.

Authors:  James T Tambong; Renlin Xu; Cynthia-Anne Kaneza; Jean-Claude Nshogozabahizi
Journal:  Evol Bioinform Online       Date:  2014-07-27       Impact factor: 1.625

5.  Analysis of the bacterial strains using Biolog plates in the contaminated soil from Riyadh community.

Authors:  Fahad Abdullah M Al-Dhabaan; Ali Hassan Bakhali
Journal:  Saudi J Biol Sci       Date:  2016-02-01       Impact factor: 4.219

6.  Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains.

Authors:  Camila Gazolla Volpiano; Fernando Hayashi Sant'Anna; Adriana Ambrosini; Jackson Freitas Brilhante de São José; Anelise Beneduzi; William B Whitman; Emanuel Maltempi de Souza; Bruno Brito Lisboa; Luciano Kayser Vargas; Luciane Maria Pereira Passaglia
Journal:  Front Microbiol       Date:  2021-03-25       Impact factor: 5.640

7.  Thainema gen. nov. (Leptolyngbyaceae, Synechococcales): A new genus of simple trichal cyanobacteria isolated from a solar saltern environment in Thailand.

Authors:  Somayeh Rasouli-Dogaheh; Jiří Komárek; Thomrat Chatchawan; Tomáš Hauer
Journal:  PLoS One       Date:  2022-01-07       Impact factor: 3.240

8.  Assigning strains to bacterial species via the internet.

Authors:  Cynthia J Bishop; David M Aanensen; Gregory E Jordan; Mogens Kilian; William P Hanage; Brian G Spratt
Journal:  BMC Biol       Date:  2009-01-26       Impact factor: 7.431

9.  Rapid identification of Brucella isolates to the species level by real time PCR based single nucleotide polymorphism (SNP) analysis.

Authors:  Krishna K Gopaul; Mark S Koylass; Catherine J Smith; Adrian M Whatmore
Journal:  BMC Microbiol       Date:  2008-06-02       Impact factor: 3.605

  9 in total

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