메뉴 건너뛰기




Volumn 38, Issue 4, 2015, Pages 209-216

Past and future species definitions for Bacteria and Archaea

Author keywords

Genomics; Species concept; Species definition

Indexed keywords

RNA 16S;

EID: 84999491381     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2015.02.001     Document Type: Review
Times cited : (401)

References (69)
  • 1
    • 43849089834 scopus 로고    scopus 로고
    • Microbial diversity and the genetic nature of microbial species
    • Achtman M., Wagner M. Microbial diversity and the genetic nature of microbial species. Nat. Rev. 2008, 6:431-440.
    • (2008) Nat. Rev. , vol.6 , pp. 431-440
    • Achtman, M.1    Wagner, M.2
  • 2
    • 0028946084 scopus 로고
    • Phylogenetic identification and detection of individual microbial cells without cultivation
    • Amann R., Ludwig W., Schleifer R. Phylogenetic identification and detection of individual microbial cells without cultivation. Microbiol. Rev. 1995, 59:143-169.
    • (1995) Microbiol. Rev. , vol.59 , pp. 143-169
    • Amann, R.1    Ludwig, W.2    Schleifer, R.3
  • 3
    • 84919421321 scopus 로고    scopus 로고
    • Whole-genome analyses: average nucleotide identity
    • Arahal D. Whole-genome analyses: average nucleotide identity. Methods Microbiol. 2014, 41:103-122.
    • (2014) Methods Microbiol. , vol.41 , pp. 103-122
    • Arahal, D.1
  • 4
    • 77949616292 scopus 로고    scopus 로고
    • Genomes as documents of evolutionary history
    • Boussau B., Daubin V. Genomes as documents of evolutionary history. Trends Ecol. Evol. 2010, 25:224-232.
    • (2010) Trends Ecol. Evol. , vol.25 , pp. 224-232
    • Boussau, B.1    Daubin, V.2
  • 6
    • 35648991375 scopus 로고    scopus 로고
    • EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences
    • Chun J., Lee J.-H., Jung Y., Kim M., Kim S., Kim B.K., Lim Y.W. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int. J. Syst. Evol. Microbiol. 2007, 57:2259-2261.
    • (2007) Int. J. Syst. Evol. Microbiol. , vol.57 , pp. 2259-2261
    • Chun, J.1    Lee, J.-H.2    Jung, Y.3    Kim, M.4    Kim, S.5    Kim, B.K.6    Lim, Y.W.7
  • 7
    • 84893495798 scopus 로고    scopus 로고
    • Integrating genomics into the taxonomy and systematics of Bacteria and Archaea
    • Chun J., Rainey F.A. Integrating genomics into the taxonomy and systematics of Bacteria and Archaea. Int. J. Syst. Evol. Microbiol. 2014, 64:316-324.
    • (2014) Int. J. Syst. Evol. Microbiol. , vol.64 , pp. 316-324
    • Chun, J.1    Rainey, F.A.2
  • 9
    • 0036407157 scopus 로고    scopus 로고
    • What are bacterial species?
    • Cohan F.M. What are bacterial species?. Annu. Rev. Microbiol. 2002, 56:457-487.
    • (2002) Annu. Rev. Microbiol. , vol.56 , pp. 457-487
    • Cohan, F.M.1
  • 10
    • 58149527706 scopus 로고    scopus 로고
    • A genomic distance based on MUM indicates discontinuity between most bacterial species and genera
    • Deloger M., El Karoui M., Petit M.-A. A genomic distance based on MUM indicates discontinuity between most bacterial species and genera. J. Bacteriol. 2009, 191:91-99.
    • (2009) J. Bacteriol. , vol.191 , pp. 91-99
    • Deloger, M.1    El Karoui, M.2    Petit, M.-A.3
  • 11
    • 66049089612 scopus 로고    scopus 로고
    • On the origin of prokaryotic species
    • Doolittle F., Zhaxybayeva O. On the origin of prokaryotic species. Genome Res. 2009, 19:755-756.
    • (2009) Genome Res. , vol.19 , pp. 755-756
    • Doolittle, F.1    Zhaxybayeva, O.2
  • 12
    • 77955580587 scopus 로고    scopus 로고
    • Darwin's solution to the species problem
    • Ereshefsky M. Darwin's solution to the species problem. Synthese 2010, 175:405-425.
    • (2010) Synthese , vol.175 , pp. 405-425
    • Ereshefsky, M.1
  • 13
    • 77956011365 scopus 로고    scopus 로고
    • Microbiology and the species problem
    • Ereshefsky M. Microbiology and the species problem. Biol. Philos. 2010, 25:553-568.
    • (2010) Biol. Philos. , vol.25 , pp. 553-568
    • Ereshefsky, M.1
  • 14
    • 84946023382 scopus 로고    scopus 로고
    • Type material in the NCBI Taxonomy Database
    • Federhen S. Type material in the NCBI Taxonomy Database. Nucl. Acids Res. 2014, 10.1093/nar/gku1127.
    • (2014) Nucl. Acids Res.
    • Federhen, S.1
  • 15
    • 34848828962 scopus 로고    scopus 로고
    • On species descriptions based on a single strain: proposal to introduce the status species proponenda (sp. pr.)
    • Felis G.E., Dellaglio F. On species descriptions based on a single strain: proposal to introduce the status species proponenda (sp. pr.). Int. J. Syst. Evol. Microbiol. 2007, 57:2185-2187.
    • (2007) Int. J. Syst. Evol. Microbiol. , vol.57 , pp. 2185-2187
    • Felis, G.E.1    Dellaglio, F.2
  • 17
    • 84864324335 scopus 로고    scopus 로고
    • Response to Gribaldo and Brochier-Armanet: time for order in microbial systematics
    • Garrity G.M., Oren A. Response to Gribaldo and Brochier-Armanet: time for order in microbial systematics. Trends Microbiol. 2012, 20:353-354.
    • (2012) Trends Microbiol. , vol.20 , pp. 353-354
    • Garrity, G.M.1    Oren, A.2
  • 19
    • 84983143193 scopus 로고    scopus 로고
    • MultiLocus sequence analysis (MLSA) in prokaryotic taxonomy
    • Glaeser S.P., Kämpfer P. MultiLocus sequence analysis (MLSA) in prokaryotic taxonomy. Syst. Appl. Microbiol. 2015, 38:237-245.
    • (2015) Syst. Appl. Microbiol. , vol.38 , pp. 237-245
    • Glaeser, S.P.1    Kämpfer, P.2
  • 22
    • 0000013908 scopus 로고    scopus 로고
    • The ideal species concept-and why we can't get it
    • Chapman & Hall, London, M.F. Claridge, H.A. Dawah, M.R. Wilson (Eds.)
    • Hull D.L. The ideal species concept-and why we can't get it. Species: the Units of Biodiversity 1997, 357-380. Chapman & Hall, London. M.F. Claridge, H.A. Dawah, M.R. Wilson (Eds.).
    • (1997) Species: the Units of Biodiversity , pp. 357-380
    • Hull, D.L.1
  • 25
    • 84919428750 scopus 로고    scopus 로고
    • Continuing importance of the phenotype in the genomic era
    • Kämpfer P. Continuing importance of the phenotype in the genomic era. Methods Microbiol. 2015, 41:307-320.
    • (2015) Methods Microbiol. , vol.41 , pp. 307-320
    • Kämpfer, P.1
  • 26
    • 84856587704 scopus 로고    scopus 로고
    • Prokaryotic taxonomy in the sequencing era - the polyphasic approach revisited
    • Kämpfer P., Glaeser S.P. Prokaryotic taxonomy in the sequencing era - the polyphasic approach revisited. Environ. Microbiol. 2012, 14:291-317.
    • (2012) Environ. Microbiol. , vol.14 , pp. 291-317
    • Kämpfer, P.1    Glaeser, S.P.2
  • 29
    • 84999592334 scopus 로고    scopus 로고
    • Classifying the uncultivated microbial majority: a place for metagenomic data in the Candidatus approach
    • Konstantinidis K., Rosselló-Móra R. Classifying the uncultivated microbial majority: a place for metagenomic data in the Candidatus approach. Syst. Appl. Microbiol. 2015, 38:223-230.
    • (2015) Syst. Appl. Microbiol. , vol.38 , pp. 223-230
    • Konstantinidis, K.1    Rosselló-Móra, R.2
  • 30
    • 14044262978 scopus 로고    scopus 로고
    • Genomic insights that advance the species definition for prokaryotes
    • Konstantinidis K., Tiedje J.M. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:2567-2592.
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 2567-2592
    • Konstantinidis, K.1    Tiedje, J.M.2
  • 31
    • 24944587193 scopus 로고    scopus 로고
    • Towards a genome-based taxonomy for prokaryotes
    • Konstantinidis K., Tiejde J.M. Towards a genome-based taxonomy for prokaryotes. J. Bacteriol. 2005, 187:6258-6264.
    • (2005) J. Bacteriol. , vol.187 , pp. 6258-6264
    • Konstantinidis, K.1    Tiejde, J.M.2
  • 33
    • 0002803581 scopus 로고    scopus 로고
    • Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systematics
    • Springer, New York, NY, D.R. Boone, R.W. Castenholz, G.M. Garrity (Eds.)
    • Ludwig W., Klenk H.-P. Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systematics. Bergey's Manual of Systematic Bacteriology 2001, 49-65. Springer, New York, NY. second ed. D.R. Boone, R.W. Castenholz, G.M. Garrity (Eds.).
    • (2001) Bergey's Manual of Systematic Bacteriology , pp. 49-65
    • Ludwig, W.1    Klenk, H.-P.2
  • 34
    • 84890634795 scopus 로고    scopus 로고
    • Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age
    • Meier-Kolthoff J.P., Klenk H.-P., Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int. J. Syst. Evol. Microbiol. 2014, 64:352-356.
    • (2014) Int. J. Syst. Evol. Microbiol. , vol.64 , pp. 352-356
    • Meier-Kolthoff, J.P.1    Klenk, H.-P.2    Göker, M.3
  • 36
    • 79951681083 scopus 로고    scopus 로고
    • Evaluation of matrix-assisted laser desorption ionization-time of flight whole cell profiles for assessing the cultivable diversity of aerobic and moderately halophilic prokaryotes thriving in solar saltern sediments
    • Munoz R., López-López A., Urdiain M., Moore E.R.B., Rosselló-Móra R. Evaluation of matrix-assisted laser desorption ionization-time of flight whole cell profiles for assessing the cultivable diversity of aerobic and moderately halophilic prokaryotes thriving in solar saltern sediments. Syst. Appl. Microbiol. 2011, 34:69-75.
    • (2011) Syst. Appl. Microbiol. , vol.34 , pp. 69-75
    • Munoz, R.1    López-López, A.2    Urdiain, M.3    Moore, E.R.B.4    Rosselló-Móra, R.5
  • 37
    • 0028082002 scopus 로고
    • Taxonomic notes: a proposal for recording the properties of putative procaryotes
    • Murray R.G.E., Schleifer K.-H. Taxonomic notes: a proposal for recording the properties of putative procaryotes. Int. J. Syst. Bacteriol. 1994, 44:174-176.
    • (1994) Int. J. Syst. Bacteriol. , vol.44 , pp. 174-176
    • Murray, R.G.E.1    Schleifer, K.-H.2
  • 38
    • 0028887837 scopus 로고
    • Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes
    • Murray R.G.E., Stackebrandt E. Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes. Int. J. Syst. Bacteriol. 1995, 45:186-187.
    • (1995) Int. J. Syst. Bacteriol. , vol.45 , pp. 186-187
    • Murray, R.G.E.1    Stackebrandt, E.2
  • 39
    • 84884207152 scopus 로고    scopus 로고
    • Burkholderia pseudomultivorans sp. nov., a novel Burkholderia cepacia complex species from human respiratory samples and the rhizosphere
    • Peeters C., Zlosnik J.E.A., Spilker T., Hird T.J., LiPuma J.J., Vandamme P. Burkholderia pseudomultivorans sp. nov., a novel Burkholderia cepacia complex species from human respiratory samples and the rhizosphere. Syst. Appl. Microbiol. 2013, 36:483-489.
    • (2013) Syst. Appl. Microbiol. , vol.36 , pp. 483-489
    • Peeters, C.1    Zlosnik, J.E.A.2    Spilker, T.3    Hird, T.J.4    LiPuma, J.J.5    Vandamme, P.6
  • 40
    • 24944484336 scopus 로고    scopus 로고
    • Fate of heterotrophic microbes in pelagic habitats: focus on populations
    • Pernthaler J., Amann R. Fate of heterotrophic microbes in pelagic habitats: focus on populations. Microbiol. Mol. Biol. Rev. 2005, 69:440-461.
    • (2005) Microbiol. Mol. Biol. Rev. , vol.69 , pp. 440-461
    • Pernthaler, J.1    Amann, R.2
  • 44
    • 1542374200 scopus 로고    scopus 로고
    • Why does the species problem still persist?
    • Reydon T.A.C. Why does the species problem still persist?. Bioessays 2004, 26:300-305.
    • (2004) Bioessays , vol.26 , pp. 300-305
    • Reydon, T.A.C.1
  • 45
    • 73149098333 scopus 로고    scopus 로고
    • Shifting the genomic gold standard for the prokaryotic species definition
    • Richter M., Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:19126-19131.
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 19126-19131
    • Richter, M.1    Rosselló-Móra, R.2
  • 46
    • 84896469548 scopus 로고    scopus 로고
    • Bypassing cultivation to identify bacterial species
    • Rodríguez-R M.L., Konstantinidis K.T. Bypassing cultivation to identify bacterial species. Microbe 2014, 9:111-118.
    • (2014) Microbe , vol.9 , pp. 111-118
    • Rodríguez-R, M.L.1    Konstantinidis, K.T.2
  • 47
    • 77949401250 scopus 로고    scopus 로고
    • Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA-DNA hybridization, proposal to combine 29 species and three subspecies as 11 genomic species
    • Rong X., Huang Y. Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA-DNA hybridization, proposal to combine 29 species and three subspecies as 11 genomic species. Int. J. Syst. Evol. Microbiol. 2010, 60:696-703.
    • (2010) Int. J. Syst. Evol. Microbiol. , vol.60 , pp. 696-703
    • Rong, X.1    Huang, Y.2
  • 48
    • 84856571925 scopus 로고    scopus 로고
    • Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories
    • Rosselló-Móra R. Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories. Environ. Microbiol. 2011, 14:318-334.
    • (2011) Environ. Microbiol. , vol.14 , pp. 318-334
    • Rosselló-Móra, R.1
  • 52
    • 33947302827 scopus 로고    scopus 로고
    • Taxonomic parameter revisited: tarnished gold standards
    • Stackebrandt E., Ebers J. Taxonomic parameter revisited: tarnished gold standards. Microbiol. Today 2006, 33:152-155.
    • (2006) Microbiol. Today , vol.33 , pp. 152-155
    • Stackebrandt, E.1    Ebers, J.2
  • 54
    • 84856214874 scopus 로고    scopus 로고
    • A call to arms for systematists: revitalising the purpose and practises underpinning the description of novel microbial taxa
    • Sutcliffe I.C., Trujillo M.E., Goodfellow M. A call to arms for systematists: revitalising the purpose and practises underpinning the description of novel microbial taxa. Ant. Van Leeuwen. 2012, 101:13-20.
    • (2012) Ant. Van Leeuwen. , vol.101 , pp. 13-20
    • Sutcliffe, I.C.1    Trujillo, M.E.2    Goodfellow, M.3
  • 58
    • 0029029166 scopus 로고
    • Taxonomic note: a pragmatic approach to the nomenclature of phenotypically similar genomic groups
    • Ursing J., Rosselló-Móra R., García-Valdés E., Lalucat J. Taxonomic note: a pragmatic approach to the nomenclature of phenotypically similar genomic groups. Int. J. Syst. Bacteriol. 1995, 45:604.
    • (1995) Int. J. Syst. Bacteriol. , vol.45 , pp. 604
    • Ursing, J.1    Rosselló-Móra, R.2    García-Valdés, E.3    Lalucat, J.4
  • 59
    • 84874323437 scopus 로고    scopus 로고
    • Achromobacter animicus sp. nov., Achromobacter mucicolens sp. nov., Achromobacter pulmonis sp. nov., Achromobacter spiritinus sp. nov., from human clinical samples
    • Vandamme P., Moore E.R.B., Cnockaert M., De Brandt E., Svensson-Stadler L., Houf K., Spilker T., LiPuma J. Achromobacter animicus sp. nov., Achromobacter mucicolens sp. nov., Achromobacter pulmonis sp. nov., Achromobacter spiritinus sp. nov., from human clinical samples. Syst. Appl. Microbiol. 2013, 36:1-10.
    • (2013) Syst. Appl. Microbiol. , vol.36 , pp. 1-10
    • Vandamme, P.1    Moore, E.R.B.2    Cnockaert, M.3    De Brandt, E.4    Svensson-Stadler, L.5    Houf, K.6    Spilker, T.7    LiPuma, J.8
  • 60
    • 84999465918 scopus 로고    scopus 로고
    • Diversity of extremely halophilic cultivable prokaryotes in Mediterranean, Atlantic and Pacific solar salterns: evidences that unexplored sites constitute sources of cultivable novelty
    • in press
    • Viver T., Cifuentes A., Díaz S., Rodríguez-Valdecantos G., González B., Antón J., Rosselló-Móra R. Diversity of extremely halophilic cultivable prokaryotes in Mediterranean, Atlantic and Pacific solar salterns: evidences that unexplored sites constitute sources of cultivable novelty. Syst. Appl. Microbiol. 2015, in press.
    • (2015) Syst. Appl. Microbiol.
    • Viver, T.1    Cifuentes, A.2    Díaz, S.3    Rodríguez-Valdecantos, G.4    González, B.5    Antón, J.6    Rosselló-Móra, R.7
  • 62
    • 79951682259 scopus 로고    scopus 로고
    • Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology
    • Welker M., Moore E.R.B. Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology. Syst. Appl. Microbiol. 2011, 34:2-11.
    • (2011) Syst. Appl. Microbiol. , vol.34 , pp. 2-11
    • Welker, M.1    Moore, E.R.B.2
  • 63
    • 84929324905 scopus 로고    scopus 로고
    • Taxonomic descriptions in the age of genomics
    • Whitman W.B. Taxonomic descriptions in the age of genomics. Syst. Appl. Microbiol. 2015, 38:217-222.
    • (2015) Syst. Appl. Microbiol. , vol.38 , pp. 217-222
    • Whitman, W.B.1
  • 64
    • 0023184331 scopus 로고
    • Bacterial evolution
    • Woese C.R. Bacterial evolution. Microbiol. Rev. 1987, 51:221-271.
    • (1987) Microbiol. Rev. , vol.51 , pp. 221-271
    • Woese, C.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.