메뉴 건너뛰기




Volumn 158, Issue 4, 2012, Pages 1005-1015

Ribosomal multilocus sequence typing: Universal characterization of bacteria from domain to strain

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA;

EID: 84859151133     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.055459-0     Document Type: Article
Times cited : (435)

References (62)
  • 1
    • 53849111617 scopus 로고    scopus 로고
    • Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens
    • Achtman, M. (2008). Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens. Annu Rev Microbiol 62, 53-70.
    • (2008) Annu Rev Microbiol , vol.62 , pp. 53-70
    • Achtman, M.1
  • 2
    • 43849089834 scopus 로고    scopus 로고
    • Microbial diversity and the genetic nature of microbial species
    • Achtman, M. & Wagner, M. (2008). Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 6, 431-440.
    • (2008) Nat Rev Microbiol , vol.6 , pp. 431-440
    • Achtman, M.1    Wagner, M.2
  • 4
    • 46049099976 scopus 로고    scopus 로고
    • Correlating ribosome function with high-resolution structures
    • Bashan, A. & Yonath, A. (2008). Correlating ribosome function with high-resolution structures. Trends Microbiol 16, 326-335.
    • (2008) Trends Microbiol , vol.16 , pp. 326-335
    • Bashan, A.1    Yonath, A.2
  • 9
    • 5644227319 scopus 로고    scopus 로고
    • Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases
    • Clarridge, J. E., III (2004). Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 17, 840-862.
    • (2004) Clin Microbiol Rev , vol.17 , pp. 840-862
    • Clarridge III, J.E.1
  • 11
    • 77956193448 scopus 로고    scopus 로고
    • progressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement
    • Darling, A. E., Mau, B. & Perna, N. T. (2010). progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5, e11147.
    • (2010) PLoS ONE , vol.5
    • Darling, A.E.1    Mau, B.2    Perna, N.T.3
  • 12
    • 35348961403 scopus 로고    scopus 로고
    • An ecological and evolutionary perspective on human-microbe mutualism and disease
    • Dethlefsen, L., McFall-Ngai, M. & Relman, D. A. (2007). An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449, 811-818.
    • (2007) Nature , vol.449 , pp. 811-818
    • Dethlefsen, L.1    McFall-Ngai, M.2    Relman, D.A.3
  • 13
    • 34249027580 scopus 로고    scopus 로고
    • Inference of bacterial microevolution using multilocus sequence data
    • Didelot, X. & Falush, D. (2007). Inference of bacterial microevolution using multilocus sequence data. Genetics 175, 1251-1266.
    • (2007) Genetics , vol.175 , pp. 1251-1266
    • Didelot, X.1    Falush, D.2
  • 15
    • 66049089612 scopus 로고    scopus 로고
    • On the origin of prokaryotic species
    • Doolittle, W. F. & Zhaxybayeva, O. (2009). On the origin of prokaryotic species. Genome Res 19, 744-756.
    • (2009) Genome Res , vol.19 , pp. 744-756
    • Doolittle, W.F.1    Zhaxybayeva, O.2
  • 16
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, 1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 17
    • 0035793056 scopus 로고    scopus 로고
    • Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences
    • other authors
    • Feil, E. J., Holmes, E. C., Bessen, D. E., Chan, M. S., Day, N. P., Enright, M. C., Goldstein, R., Hood, D. W., Kalia, A. & other authors (2001). Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences. Proc Natl Acad Sci U S A 98, 182-187.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 182-187
    • Feil, E.J.1    Holmes, E.C.2    Bessen, D.E.3    Chan, M.S.4    Day, N.P.5    Enright, M.C.6    Goldstein, R.7    Hood, D.W.8    Kalia, A.9
  • 18
    • 59849086092 scopus 로고    scopus 로고
    • The bacterial species challenge: Making sense of genetic and ecological diversity
    • Fraser, C., Alm, E. J., Polz, M. F., Spratt, B. G. & Hanage, W. P. (2009). The bacterial species challenge: making sense of genetic and ecological diversity. Science 323, 741-746.
    • (2009) Science , vol.323 , pp. 741-746
    • Fraser, C.1    Alm, E.J.2    Polz, M.F.3    Spratt, B.G.4    Hanage, W.P.5
  • 19
    • 0002232560 scopus 로고    scopus 로고
    • Genomic analysis of the genes encoding ribosomal proteins in eight eubacterial species and Saccharomyces cerevisiae
    • Fujita, K., Baba, T. & Isono, K. (1998). Genomic analysis of the genes encoding ribosomal proteins in eight eubacterial species and Saccharomyces cerevisiae. Genome Inform Ser Workshop Genome Inform 9, 3-12.
    • (1998) Genome Inform Ser Workshop Genome Inform , vol.9 , pp. 3-12
    • Fujita, K.1    Baba, T.2    Isono, K.3
  • 21
    • 79953007909 scopus 로고    scopus 로고
    • Microbial metagenomics: Beyond the genome
    • Gilbert, J. A. & Dupont, C. L. (2011). Microbial metagenomics: beyond the genome. Annu Rev Mar Sci 3, 347-371.
    • (2011) Annu Rev Mar Sci , vol.3 , pp. 347-371
    • Gilbert, J.A.1    Dupont, C.L.2
  • 22
    • 0029660135 scopus 로고    scopus 로고
    • Phylogenetic analysis of the bacterial communities in marine sediments
    • Gray, J. P. & Herwig, R. P. (1996). Phylogenetic analysis of the bacterial communities in marine sediments. Appl Environ Microbiol 62, 4049-4059.
    • (1996) Appl Environ Microbiol , vol.62 , pp. 4049-4059
    • Gray, J.P.1    Herwig, R.P.2
  • 23
    • 0033859839 scopus 로고    scopus 로고
    • Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: Influence of excluding poorly alignable sites from analysis
    • Hansmann, S. & Martin, W. (2000). Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis. Int J Syst Evol Microbiol 50, 1655-1663.
    • (2000) Int J Syst Evol Microbiol , vol.50 , pp. 1655-1663
    • Hansmann, S.1    Martin, W.2
  • 25
    • 0033053213 scopus 로고    scopus 로고
    • The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis
    • Holmes, E. C., Urwin, R. & Maiden, M. C. J. (1999). The influence of recombination on the population structure and evolution of the human pathogen Neisseria meningitidis. Mol Biol Evol 16, 741-749.
    • (1999) Mol Biol Evol , vol.16 , pp. 741-749
    • Holmes, E.C.1    Urwin, R.2    Maiden, M.C.J.3
  • 26
    • 0025063184 scopus 로고
    • Reproducibility and indices of discriminatory power of microbial typing methods
    • Hunter, P. R. (1990). Reproducibility and indices of discriminatory power of microbial typing methods. J Clin Microbiol 28, 1903-1905.
    • (1990) J Clin Microbiol , vol.28 , pp. 1903-1905
    • Hunter, P.R.1
  • 27
    • 0023738045 scopus 로고
    • Numerical index of the discriminatory ability of typing systems: An application of Simpson's index of diversity
    • Hunter, P. R. & Gaston, M. A. (1988). Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J Clin Microbiol 26, 2465-2466.
    • (1988) J Clin Microbiol , vol.26 , pp. 2465-2466
    • Hunter, P.R.1    Gaston, M.A.2
  • 28
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • Huson, D. H. & Bryant, D. (2006). Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23, 254-267.
    • (2006) Mol Biol Evol , vol.23 , pp. 254-267
    • Huson, D.H.1    Bryant, D.2
  • 30
    • 78650827616 scopus 로고    scopus 로고
    • BIGSdb: Scalable analysis of bacterial genome variation at the population level
    • Jolley, K. A. & Maiden, M. C. (2010). BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11, 595.
    • (2010) BMC Bioinformatics , vol.11 , pp. 595
    • Jolley, K.A.1    Maiden, M.C.2
  • 31
    • 4444308959 scopus 로고    scopus 로고
    • Anthrax molecular epidemiology and forensics: Using the appropriate marker for different evolutionary scales
    • Keim, P., Van Ert, M. N., Pearson, T., Vogler, A. J., Huynh, L. Y. & Wagner, D. M. (2004). Anthrax molecular epidemiology and forensics: using the appropriate marker for different evolutionary scales. Infect Genet Evol 4, 205-213.
    • (2004) Infect Genet Evol , vol.4 , pp. 205-213
    • Keim, P.1    van Ert, M.N.2    Pearson, T.3    Vogler, A.J.4    Huynh, L.Y.5    Wagner, D.M.6
  • 33
    • 45949109669 scopus 로고    scopus 로고
    • MEGA: A biologistcentric software for evolutionary analysis of DNA and protein sequences
    • Kumar, S., Nei, M., Dudley, J. & Tamura, K. (2008). MEGA: a biologistcentric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9, 299-306.
    • (2008) Brief Bioinform , vol.9 , pp. 299-306
    • Kumar, S.1    Nei, M.2    Dudley, J.3    Tamura, K.4
  • 35
    • 79960004119 scopus 로고    scopus 로고
    • Interactive Tree Of Life v2: Online annotation and display of phylogenetic trees made easy
    • (Web Server issue)
    • Letunic, I. & Bork, P. (2011). Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39 (Web Server issue), W475-W478.
    • (2011) Nucleic Acids Res , vol.39
    • Letunic, I.1    Bork, P.2
  • 36
    • 0027319339 scopus 로고
    • Application of rRNA-based probes for observing marine nanoplanktonic protists
    • Lim, E. L., Amaral, L. A., Caron, D. A. & DeLong, E. F. (1993). Application of rRNA-based probes for observing marine nanoplanktonic protists. Appl Environ Microbiol 59, 1647-1655.
    • (1993) Appl Environ Microbiol , vol.59 , pp. 1647-1655
    • Lim, E.L.1    Amaral, L.A.2    Caron, D.A.3    DeLong, E.F.4
  • 37
    • 33750290454 scopus 로고    scopus 로고
    • Multilocus sequence typing of bacteria
    • Maiden, M. C. (2006). Multilocus sequence typing of bacteria. Annu Rev Microbiol 60, 561-588.
    • (2006) Annu Rev Microbiol , vol.60 , pp. 561-588
    • Maiden, M.C.1
  • 38
    • 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. J., 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.J.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
  • 41
    • 0034963344 scopus 로고    scopus 로고
    • Nomenclature of major antimicrobialresistant clones of Streptococcus pneumoniae defined by the pneumococcal molecular epidemiology network
    • other authors
    • McGee, L., McDougal, L., Zhou, J., Spratt, B. G., Tenover, F. C., George, R., Hakenbeck, R., Hryniewicz, W., Lefévre, J. C. & other authors (2001). Nomenclature of major antimicrobialresistant clones of Streptococcus pneumoniae defined by the pneumococcal molecular epidemiology network. J Clin Microbiol 39, 2565-2571.
    • (2001) J Clin Microbiol , vol.39 , pp. 2565-2571
    • McGee, L.1    McDougal, L.2    Zhou, J.3    Spratt, B.G.4    Tenover, F.C.5    George, R.6    Hakenbeck, R.7    Hryniewicz, W.8    Lefévre, J.C.9
  • 45
    • 0022507362 scopus 로고
    • Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
    • Nei, M. & Gojobori, T. (1986). Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3, 418-426.
    • (1986) Mol Biol Evol , vol.3 , pp. 418-426
    • Nei, M.1    Gojobori, T.2
  • 47
  • 48
    • 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
  • 50
  • 53
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28, 2731-2739.
    • (2011) Mol Biol Evol , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5    Kumar, S.6
  • 54
    • 33645464254 scopus 로고    scopus 로고
    • RibAlign: A software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits
    • Teeling, H. & Gloeckner, F. O. (2006). RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits. BMC Bioinformatics 7, 66.
    • (2006) BMC Bioinformatics , vol.7 , pp. 66
    • Teeling, H.1    Gloeckner, F.O.2
  • 57
    • 0023184331 scopus 로고
    • Bacterial evolution
    • Woese, C. R. (1987). Bacterial evolution. Microbiol Rev 51, 221-271.
    • (1987) Microbiol Rev , vol.51 , pp. 221-271
    • Woese, C.R.1
  • 58
    • 0025300402 scopus 로고
    • Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya
    • Woese, C. R., Kandler, O. & Wheelis, M. L. (1990). Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A 87, 4576-4579.
    • (1990) Proc Natl Acad Sci U S A , vol.87 , pp. 4576-4579
    • Woese, C.R.1    Kandler, O.2    Wheelis, M.L.3
  • 59
    • 50149086330 scopus 로고    scopus 로고
    • An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP)
    • Wu, D. Y., Hartman, A., Ward, N. & Eisen, J. A. (2008). An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS ONE 3, e2566.
    • (2008) PLoS ONE , vol.3
    • Wu, D.Y.1    Hartman, A.2    Ward, N.3    Eisen, J.A.4
  • 61
    • 77956967295 scopus 로고    scopus 로고
    • Using the Velvet de novo assembler for shortread sequencing technologies
    • 11.5
    • Zerbino, D. R. (2010). Using the Velvet de novo assembler for shortread sequencing technologies. Curr Protoc Bioinformatics 11, 11.5.
    • (2010) Curr Protoc Bioinformatics , pp. 11
    • Zerbino, D.R.1
  • 62
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino, D. R. & Birney, E. (2008). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18, 821-829.
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.