Literature DB >> 17020593

Genomics and the bacterial species problem.

W Ford Doolittle1, R Thane Papke.   

Abstract

Whether or not bacteria have species is a perennially vexatious question. Given what we now know about variation among bacterial genomes, we argue that there is no intrinsic reason why the processes driving diversification and adaptation must produce groups of individuals sufficiently coherent in their genetic and phenotypic properties to merit the designation 'species'--although sometimes they might.

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Year:  2006        PMID: 17020593      PMCID: PMC1794555          DOI: 10.1186/gb-2006-7-9-116

Source DB:  PubMed          Journal:  Genome Biol        ISSN: 1474-7596            Impact factor:   13.583


  31 in total

Review 1.  Phylogenetic classification and the universal tree.

Authors:  W F Doolittle
Journal:  Science       Date:  1999-06-25       Impact factor: 47.728

Review 2.  Recombination and the population structures of bacterial pathogens.

Authors:  E J Feil; B G Spratt
Journal:  Annu Rev Microbiol       Date:  2001       Impact factor: 15.500

3.  The mind of the species problem.

Authors:  J Hey
Journal:  Trends Ecol Evol       Date:  2001-07-01       Impact factor: 17.712

4.  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

Review 5.  Genomic islands in pathogenic and environmental microorganisms.

Authors:  Ulrich Dobrindt; Bianca Hochhut; Ute Hentschel; Jörg Hacker
Journal:  Nat Rev Microbiol       Date:  2004-05       Impact factor: 60.633

Review 6.  Insights on biology and evolution from microbial genome sequencing.

Authors:  Claire M Fraser-Liggett
Journal:  Genome Res       Date:  2005-12       Impact factor: 9.043

7.  Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast.

Authors:  J A Heinemann; G F Sprague
Journal:  Nature       Date:  1989-07-20       Impact factor: 49.962

8.  Recombination in Escherichia coli and the definition of biological species.

Authors:  D E Dykhuizen; L Green
Journal:  J Bacteriol       Date:  1991-11       Impact factor: 3.490

9.  Evolutionary origins of genomic repertoires in bacteria.

Authors:  Emmanuelle Lerat; Vincent Daubin; Howard Ochman; Nancy A Moran
Journal:  PLoS Biol       Date:  2005-04-05       Impact factor: 8.029

10.  Fuzzy species among recombinogenic bacteria.

Authors:  William P Hanage; Christophe Fraser; Brian G Spratt
Journal:  BMC Biol       Date:  2005-03-07       Impact factor: 7.431

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  68 in total

Review 1.  Microbial Speciation.

Authors:  B Jesse Shapiro; Martin F Polz
Journal:  Cold Spring Harb Perspect Biol       Date:  2015-09-09       Impact factor: 10.005

2.  Pattern pluralism and the Tree of Life hypothesis.

Authors:  W Ford Doolittle; Eric Bapteste
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-29       Impact factor: 11.205

Review 3.  Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases.

Authors:  Daniel A Peterson; Daniel N Frank; Norman R Pace; Jeffrey I Gordon
Journal:  Cell Host Microbe       Date:  2008-06-12       Impact factor: 21.023

4.  From aneuploidy to cancer: the evolution of a new species?

Authors:  Samuel Knauss; Andreas Klein
Journal:  J Biosci       Date:  2012-06       Impact factor: 1.826

5.  In silico prediction of human pathogenicity in the γ-proteobacteria.

Authors:  Massimo Andreatta; Morten Nielsen; Frank Møller Aarestrup; Ole Lund
Journal:  PLoS One       Date:  2010-10-27       Impact factor: 3.240

6.  Gene and genome trees conflict at many levels.

Authors:  Leanne S Haggerty; Fergal J Martin; David A Fitzpatrick; James O McInerney
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2009-08-12       Impact factor: 6.237

7.  Merging taxonomy with ecological population prediction in a case study of Vibrionaceae.

Authors:  Sarah P Preheim; Sonia Timberlake; Martin F Polz
Journal:  Appl Environ Microbiol       Date:  2011-08-26       Impact factor: 4.792

8.  Co-assortment in integron-associated gene cassette assemblages in environmental DNA samples.

Authors:  Carolyn A Michael; Nigel R Andrew
Journal:  BMC Genet       Date:  2010-08-10       Impact factor: 2.797

Review 9.  The dynamic genetic repertoire of microbial communities.

Authors:  Paul Wilmes; Sheri L Simmons; Vincent J Denef; Jillian F Banfield
Journal:  FEMS Microbiol Rev       Date:  2008-11-24       Impact factor: 16.408

10.  On the origins of a Vibrio species.

Authors:  Tammi Vesth; Trudy M Wassenaar; Peter F Hallin; Lars Snipen; Karin Lagesen; David W Ussery
Journal:  Microb Ecol       Date:  2010-01       Impact factor: 4.552

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