메뉴 건너뛰기




Volumn 64, Issue PART 2, 2014, Pages 316-324

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

EID: 84893495798     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.054171-0     Document Type: Review
Times cited : (438)

References (63)
  • 3
    • 33750953227 scopus 로고    scopus 로고
    • Whole-genome re-sequencing
    • Bentley, D. R. (2006). Whole-genome re-sequencing. Curr Opin Genet Dev 16, 545-552.
    • (2006) Curr Opin Genet Dev , vol.16 , pp. 545-552
    • Bentley, D.R.1
  • 6
    • 84872836707 scopus 로고    scopus 로고
    • Defining bacterial species in the genomic era: Insights from the genus Acinetobacter
    • Chan, J. Z.-M., Halachev, M. R., Loman, N. J., Constantinidou, C. & Pallen, M. J. (2012). Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC Microbiol 12, 302.
    • (2012) BMC Microbiol , vol.12 , pp. 302
    • Chan, J.Z.-M.1    Halachev, M.R.2    Loman, N.J.3    Constantinidou, C.4    Pallen, M.J.5
  • 7
    • 70349304423 scopus 로고    scopus 로고
    • Comparative genomics reveals mechanism for short-term and longterm clonal transitions in pandemic Vibrio cholerae
    • other authors
    • Chun, J., Grim, C. J., Hasan, N. A., Lee, J. H., Choi, S. Y., Haley, B. J., Taviani, E., Jeon, Y. S., Kim, D. W. & other authors (2009). Comparative genomics reveals mechanism for short-term and longterm clonal transitions in pandemic Vibrio cholerae. Proc Natl Acad Sci U S A 106, 15442-15447.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 15442-15447
    • Chun, J.1    Grim, C.J.2    Hasan, N.A.3    Lee, J.H.4    Choi, S.Y.5    Haley, B.J.6    Taviani, E.7    Jeon, Y.S.8    Kim, D.W.9
  • 9
    • 0014868747 scopus 로고
    • Polyphasic taxonomy of the genus Vibrio: Numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species
    • Colwell, R. R. (1970). Polyphasic taxonomy of the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacteriol 104, 410-433.
    • (1970) J Bacteriol , vol.104 , pp. 410-433
    • Colwell, R.R.1
  • 11
    • 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. (2009). A genomic distance based on MUM indicates discontinuity between most bacterial species and genera. J Bacteriol 191, 91-99.
    • (2009) J Bacteriol , vol.191 , pp. 91-99
    • Deloger, M.1    El Karoui, M.2    Petit, M.A.3
  • 14
    • 0026585263 scopus 로고
    • How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity
    • Fox, G. E., Wisotzkey, J. D. & Jurtshuk, P., Jr (1992). How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42, 166-170.
    • (1992) Int J Syst Bacteriol , vol.42 , pp. 166-170
    • Fox, G.E.1    Wisotzkey, J.D.2    Jurtshuk Jr., P.3
  • 16
    • 40449120034 scopus 로고    scopus 로고
    • A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: Use of multilocus sequence analysis for streptomycete systematics
    • Guo, Y., Zheng, W., Rong, X. & Huang, Y. (2008). A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics. Int J Syst Evol Microbiol 58, 149-159.
    • (2008) Int J Syst Evol Microbiol , vol.58 , pp. 149-159
    • Guo, Y.1    Zheng, W.2    Rong, X.3    Huang, Y.4
  • 19
    • 84882669481 scopus 로고    scopus 로고
    • Environmental microbiology: Exploring diversity with single-cell genomics
    • Hofer, U. (2013). Environmental microbiology: exploring diversity with single-cell genomics. Nat Rev Microbiol 11, 598-599.
    • (2013) Nat Rev Microbiol , vol.11 , pp. 598-599
    • Hofer, U.1
  • 21
    • 84893484703 scopus 로고    scopus 로고
    • EzEditor: A versatile sequence alignment editor for both ribosomal RNA and protein coding genes
    • (in press)
    • Jeon, Y.-S., Lee, K., Park, S.-C., Kim, B.-S., Cho, Y.-J., Ha, S.-M. & Chun, J. (2014). EzEditor: a versatile sequence alignment editor for both ribosomal RNA and protein coding genes. Int J Syst Evol Microbiol 64 (in press).
    • (2014) Int J Syst Evol Microbiol , vol.64
    • Jeon, Y.-S.1    Lee, K.2    Park, S.-C.3    Kim, B.-S.4    Cho, Y.-J.5    Ha, S.-M.6    Chun, J.7
  • 22
    • 84881665892 scopus 로고    scopus 로고
    • Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group, and pairwise genome comparisons of the species of the group by means of ANI calculations
    • other authors
    • Jiménez, G., Urdiain, M., Cifuentes, A., López-López, A., Blanch, A. R., Tamames, J., Kämpfer, P., Kolstø, A. B., Ramón, D. & other authors (2013). Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group, and pairwise genome comparisons of the species of the group by means of ANI calculations. Syst Appl Microbiol 36, 383-391.
    • (2013) Syst Appl Microbiol , vol.36 , pp. 383-391
    • Jiménez, G.1    Urdiain, M.2    Cifuentes, A.3    López-López, A.4    Blanch, A.R.5    Tamames, J.6    Kämpfer, P.7    Kolstø, A.B.8    Ramón, D.9
  • 23
    • 0014264517 scopus 로고
    • Deoxyribonucleic acid homology in bacterial taxonomy: Effect of incubation temperature on reaction specificity
    • Johnson, J. L. & Ordal, E. J. (1968). Deoxyribonucleic acid homology in bacterial taxonomy: effect of incubation temperature on reaction specificity. J Bacteriol 95, 893-900.
    • (1968) J Bacteriol , vol.95 , pp. 893-900
    • Johnson, J.L.1    Ordal, E.J.2
  • 24
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent, W. J. (2002). BLAT-the BLAST-like alignment tool. Genome Res 12, 656-664.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 25
    • 84863230041 scopus 로고    scopus 로고
    • Introducing EzTaxon-e: A prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species
    • other authors
    • Kim, O. S., Cho, Y. J., Lee, K., Yoon, S. H., Kim, M., Na, H., Park, S. C., Jeon, Y. S., Lee, J. H. & other authors (2012). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62, 716-721.
    • (2012) Int J Syst Evol Microbiol , vol.62 , pp. 716-721
    • Kim, O.S.1    Cho, Y.J.2    Lee, K.3    Yoon, S.H.4    Kim, M.5    Na, H.6    Park, S.C.7    Jeon, Y.S.8    Lee, J.H.9
  • 26
    • 84893511241 scopus 로고    scopus 로고
    • Towards a taxanomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
    • Kim, M., Oh, H.-S., Park, S.-C. & Chun, J. (2014a). Towards a taxanomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64, 346-351.
    • (2014) Int J Syst Evol Microbiol , vol.64 , pp. 346-351
    • Kim, M.1    Oh, H.-S.2    Park, S.-C.3    Chun, J.4
  • 27
    • 84893432387 scopus 로고    scopus 로고
    • Applications of next-generation sequencing to unravelling the evolutionary history of algae
    • Kim, K. M., Park, J.-H., Bhattacharya, D. & Yoon, H. S. (2014b). Applications of next-generation sequencing to unravelling the evolutionary history of algae. Int J Syst Evol Microbiol 64, 333-345.
    • (2014) Int J Syst Evol Microbiol , vol.64 , pp. 333-345
    • Kim, K.M.1    Park, J.-H.2    Bhattacharya, D.3    Yoon, H.S.4
  • 28
    • 14044262978 scopus 로고    scopus 로고
    • Genomic insights that advance the species definition for prokaryotes
    • Konstantinidis, K. T. & Tiedje, J. M. (2005). Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 102, 2567-2572.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 2567-2572
    • Konstantinidis, K.T.1    Tiedje, J.M.2
  • 31
    • 84893430996 scopus 로고    scopus 로고
    • Use of gene sequence analyses and genome comparisons for yeast systematics
    • Kurtzman, C. P. (2014). Use of gene sequence analyses and genome comparisons for yeast systematics. Int J Syst Evol Microbiol 64, 325-332.
    • (2014) Int J Syst Evol Microbiol , vol.64 , pp. 325-332
    • Kurtzman, C.P.1
  • 32
    • 84876732832 scopus 로고    scopus 로고
    • Phylogeny of bacterial and archaeal genomes using conserved genes: Supertrees and supermatrices
    • Lang, J. M., Darling, A. E. & Eisen, J. A. (2013). Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLoS ONE 8, e62510.
    • (2013) PLoS ONE , vol.8
    • Lang, J.M.1    Darling, A.E.2    Eisen, J.A.3
  • 33
    • 84889583341 scopus 로고    scopus 로고
    • Flavobacterium limnosediminis sp. nov., isolated from sediment of a freshwater lake
    • Lee, K., Park, S. C., Yi, H. & Chun, J. (2013). Flavobacterium limnosediminis sp. nov., isolated from sediment of a freshwater lake. Int J Syst Evol Microbiol 63, 4784-4789.
    • (2013) Int J Syst Evol Microbiol , vol.63 , pp. 4784-4789
    • Lee, K.1    Park, S.C.2    Yi, H.3    Chun, J.4
  • 34
    • 84874041126 scopus 로고    scopus 로고
    • Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi
    • Löffler, F. E., Yan, J., Ritalahti, K. M., Adrian, L., Edwards, E. A., Konstantinidis, K. T., Müller, J. A., Fullerton, H., Zinder, S. H. & Spormann, A. M. (2013). Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi. Int J Syst Evol Microbiol 63, 625-635.
    • (2013) Int J Syst Evol Microbiol , vol.63 , pp. 625-635
    • Löffler, F.E.1    Yan, J.2    Ritalahti, K.M.3    Adrian, L.4    Edwards, E.A.5    Konstantinidis, K.T.6    Müller, J.A.7    Fullerton, H.8    Zinder, S.H.9    Spormann, A.M.10
  • 35
    • 84868690436 scopus 로고    scopus 로고
    • Vibrio aestivus sp. nov. and Vibrio quintilis sp. nov., related to Marisflavi and Gazogenes clades, respectively
    • Lucena, T., Ruvira, M. A., Arahal, D. R., Macián, M. C. & Pujalte, M. J. (2012). Vibrio aestivus sp. nov. and Vibrio quintilis sp. nov., related to Marisflavi and Gazogenes clades, respectively. Syst Appl Microbiol 35, 427-431.
    • (2012) Syst Appl Microbiol , vol.35 , pp. 427-431
    • Lucena, T.1    Ruvira, M.A.2    Arahal, D.R.3    Macián, M.C.4    Pujalte, M.J.5
  • 36
    • 13144252236 scopus 로고    scopus 로고
    • Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms
    • other authors
    • Maiden, M. C., Bygraves, J. A., Feil, E., Morelli, G., Russell, J. E., Urwin, R., Zhang, Q., Zhou, J., Zurth, K. & other authors (1998). Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 95, 3140-3145.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , pp. 3140-3145
    • Maiden, M.C.1    Bygraves, J.A.2    Feil, E.3    Morelli, G.4    Russell, J.E.5    Urwin, R.6    Zhang, Q.7    Zhou, J.8    Zurth, K.9
  • 38
    • 84884367050 scopus 로고    scopus 로고
    • Phylogeny and classification of Dickeya based on multilocus sequence analysis
    • Marrero, G., Schneider, K. L., Jenkins, D. M. & Alvarez, A. M. (2013). Phylogeny and classification of Dickeya based on multilocus sequence analysis. Int J Syst Evol Microbiol 63, 3524-3539.
    • (2013) Int J Syst Evol Microbiol , vol.63 , pp. 3524-3539
    • Marrero, G.1    Schneider, K.L.2    Jenkins, D.M.3    Alvarez, A.M.4
  • 40
    • 84874011652 scopus 로고    scopus 로고
    • Genome sequence-based species delimitation with confidence intervals and improved distance functions
    • Meier-Kolthoff, J. P., Auch, A. F., Klenk, H. P. & Göker, M. (2013). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14, 60.
    • (2013) BMC Bioinformatics , vol.14 , pp. 60
    • Meier-Kolthoff, J.P.1    Auch, A.F.2    Klenk, H.P.3    Göker, M.4
  • 41
    • 84890634795 scopus 로고    scopus 로고
    • Taxanomic use of DNA G+C content and DNA-DNA hybridization in the genomic age
    • Meier-Kolthoff, J. P., Klenk, H.-P. & Göker, M. (2014). Taxanomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 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
  • 42
    • 84883464181 scopus 로고    scopus 로고
    • Accurate and universal delineation of prokaryotic species
    • Mende, D. R., Sunagawa, S., Zeller, G. & Bork, P. (2013). Accurate and universal delineation of prokaryotic species. Nat Methods 10, 881-884.
    • (2013) Nat Methods , vol.10 , pp. 881-884
    • Mende, D.R.1    Sunagawa, S.2    Zeller, G.3    Bork, P.4
  • 43
    • 84893518970 scopus 로고    scopus 로고
    • Conserved signature indels and signature proteins as novel tools for understanding microbioal phylogeny and systematics: Identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria
    • Naushad, H. S., Lee, B. & Gupta, R. S. (2014). Conserved signature indels and signature proteins as novel tools for understanding microbioal phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria. Int J Syst Evol Microbiol 64, 366-383.
    • (2014) Int J Syst Evol Microbiol , vol.64 , pp. 366-383
    • Naushad, H.S.1    Lee, B.2    Gupta, R.S.3
  • 46
    • 73149098333 scopus 로고    scopus 로고
    • Shifting the genomic gold standard for the prokaryotic species definition
    • Richter, M. & Rosselló-Móra, R. (2009). Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106, 19126-19131.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 19126-19131
    • Richter, M.1    Rosselló-Móra, R.2
  • 48
    • 84900241743 scopus 로고    scopus 로고
    • DNA-DNA reassociation methods applied to microbial taxonomy and their critical evaluation
    • In, Edited by E. Stackebrandt. Berlin, Heidelberg: Springer
    • Rosselló-Mora, R. (2006). DNA-DNA reassociation methods applied to microbial taxonomy and their critical evaluation. In Molecular Identification, Systematics and Population Structure of Prokaryotes, pp. 23-50. Edited by E. Stackebrandt. Berlin, Heidelberg: Springer.
    • (2006) Molecular Identification, Systematics and Population Structure of Prokaryotes , pp. 23-50
    • Rosselló-Mora, R.1
  • 49
  • 50
    • 84876346702 scopus 로고    scopus 로고
    • Marinifilum flexuosum sp. nov., a new Bacteroidetes isolated from coastal Mediterranean Sea water and emended description of the genus Marinifilum Na et al., 2009
    • Ruvira, M. A., Lucena, T., Pujalte, M. J., Arahal, D. R. & Macián, M. C. (2013). Marinifilum flexuosum sp. nov., a new Bacteroidetes isolated from coastal Mediterranean Sea water and emended description of the genus Marinifilum Na et al., 2009. Syst Appl Microbiol 36, 155-159.
    • (2013) Syst Appl Microbiol , vol.36 , pp. 155-159
    • Ruvira, M.A.1    Lucena, T.2    Pujalte, M.J.3    Arahal, D.R.4    Macián, M.C.5
  • 52
    • 33947302827 scopus 로고    scopus 로고
    • Taxonomic parameters revisited: Tarnished gold standards
    • Stackebrandt, E. & Ebers, J. (2006). Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33, 152-155.
    • (2006) Microbiol Today , vol.33 , pp. 152-155
    • Stackebrandt, E.1    Ebers, J.2
  • 53
    • 0028028182 scopus 로고
    • Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology
    • Stackebrandt, E. & Goebel, B. M. (1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846-849.
    • (1994) Int J Syst Bacteriol , vol.44 , pp. 846-849
    • Stackebrandt, E.1    Goebel, B.M.2
  • 55
    • 26244450604 scopus 로고    scopus 로고
    • Multilocus sequence typing: Data analysis in clinical microbiology and public health
    • Sullivan, C. B., Diggle, M. A. & Clarke, S. C. (2005). Multilocus sequence typing: data analysis in clinical microbiology and public health. Mol Biotechnol 29, 245-254.
    • (2005) Mol Biotechnol , vol.29 , pp. 245-254
    • Sullivan, C.B.1    Diggle, M.A.2    Clarke, S.C.3
  • 62
    • 84874333859 scopus 로고    scopus 로고
    • Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names
    • other authors
    • Yarza, P., Spröer, C., Swiderski, J., Mrotzek, N., Spring, S., Tindall, B. J., Gronow, S., Pukall, R., Klenk, H. P. & other authors (2013). Sequencing orphan species initiative (SOS): filling the gaps in the 16S rRNA gene sequence database for all species with validly published names. Syst Appl Microbiol 36, 69-73.
    • (2013) Syst Appl Microbiol , vol.36 , pp. 69-73
    • Yarza, P.1    Spröer, C.2    Swiderski, J.3    Mrotzek, N.4    Spring, S.5    Tindall, B.J.6    Gronow, S.7    Pukall, R.8    Klenk, H.P.9
  • 63
    • 84857234269 scopus 로고    scopus 로고
    • Comparative genomics of Neisseria weaveri clarifies the taxonomy of this species and identifies genetic determinants that may be associated with virulence
    • Yi, H., Cho, Y. J., Yoon, S. H., Park, S. C. & Chun, J. (2012). Comparative genomics of Neisseria weaveri clarifies the taxonomy of this species and identifies genetic determinants that may be associated with virulence. FEMS Microbiol Lett 328, 100-105.
    • (2012) FEMS Microbiol Lett , vol.328 , pp. 100-105
    • Yi, H.1    Cho, Y.J.2    Yoon, S.H.3    Park, S.C.4    Chun, J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.