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Volumn 106, Issue 1, 2014, Pages 43-56

Then and now: A systematic review of the systematics of prokaryotes in the last 80 years

Author keywords

Antonie van Leeuwenhoek; DNA DNA reassociation; Genomics; History of prokaryotes; Polyphasic taxonomy; Species concept

Indexed keywords

GENOMIC DNA; RNA 16S;

EID: 84903985430     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-013-0084-1     Document Type: Article
Times cited : (80)

References (70)
  • 1
    • 1842747406 scopus 로고
    • Studies upon the methane fermentation. IV. The isolation and culture of Methanobacterium Omelianskii
    • Barker HA (1939/1940) Studies upon the methane fermentation. IV. The isolation and culture of Methanobacterium Omelianskii . Antonie van Leeuwenhoek 6:201-210
    • (1939) Antonie Van Leeuwenhoek , vol.6 , pp. 201-210
    • Barker, H.A.1
  • 3
    • 0031765486 scopus 로고    scopus 로고
    • A small, dilute-cytoplasm, high-affinity, novel bacterium isolated by extinction culture and having kinetic constants compatible with growth at ambient concentrations of dissolved nutrients in seawater
    • Baltimore Button DK, Robertson BR, Lepp PW, Schmidt TM (1998) A small, dilute-cytoplasm, high-affinity, novel bacterium isolated by extinction culture and having kinetic constants compatible with growth at ambient concentrations of dissolved nutrients in seawater. Appl Environ Microbiol 64:4467-4476 (Pubitemid 28538019)
    • (1998) Applied and Environmental Microbiology , vol.64 , Issue.11 , pp. 4467-4476
    • Button, D.K.1    Robertson, B.R.2    Lepp, P.W.3    Schmidt, T.M.4
  • 5
    • 0035200743 scopus 로고    scopus 로고
    • Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify Recommendation 30b of the Bacteriological Code (1990 Revision)
    • Christensen H, Bisgaard M, Frederiksen W, Mutters R, Kuhnert P, Olsen JE (2001) Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify recommendation 30b of the Bacteriological Code (1990 revision). Int J Syst Evol Microbiol 51:2221-2225 (Pubitemid 33107442)
    • (2001) International Journal of Systematic and Evolutionary Microbiology , vol.51 , Issue.6 , pp. 2221-2225
    • Christensen, H.1    Bisgaard, M.2    Frederiksen, W.3    Mutters, R.4    Kuhnert, P.5    Olsen, J.E.6
  • 7
    • 0003150362 scopus 로고
    • Polyphasic taxonomy of bacteria
    • Iizuka H, Hazegawa T (eds) University of Tokyo Press, Tokyo
    • Colwell RR (1970) Polyphasic taxonomy of bacteria. In: Iizuka H, Hazegawa T (eds) Culture collections of microorganisms. University of Tokyo Press, Tokyo, pp 421-436
    • (1970) Culture Collections of Microorganisms , pp. 421-436
    • Colwell, R.R.1
  • 8
    • 0036324056 scopus 로고    scopus 로고
    • High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates
    • DOI 10.1128/AEM.68.8.3878-3885.2002
    • Connon SA, Giovannoni SJ (2002) High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 68:3878-3885 (Pubitemid 34836698)
    • (2002) Applied and Environmental Microbiology , vol.68 , Issue.8 , pp. 3878-3885
    • Connon, S.A.1    Giovannoni, S.J.2
  • 11
    • 34250610200 scopus 로고
    • Bacterium pneumoniae en Bacterium lactis aerogenes
    • de Graaff WC (1936) Bacterium pneumoniae en Bacterium lactis aerogenes. Antonie van Leeuwenhoek 3:18-27
    • (1936) Antonie Van Leeuwenhoek , vol.3 , pp. 18-27
    • De Graaff, W.C.1
  • 12
    • 83155188445 scopus 로고    scopus 로고
    • Multilocus sequence determination and analysis
    • Rainey FA, Oren A (eds) Elsevier, Amsterdam
    • De Vos P (2011) Multilocus sequence determination and analysis. In: Rainey FA, Oren A (eds) Taxonomy of prokaryotes - methods in microbiology, vol 38. Elsevier, Amsterdam, pp 385-407
    • (2011) Taxonomy of Prokaryotes - Methods in Microbiology , vol.38 , pp. 385-407
    • De Vos, P.1
  • 15
    • 34848828962 scopus 로고    scopus 로고
    • On species descriptions based on a single strain: Proposal to introduce the status species proponenda (sp. pr.)
    • DOI 10.1099/ijs.0.64931-0
    • Felis GE, Dellaglio F (2007) On species descriptions based on a single strain: proposal to introduce the status species proponenda (sp. pr.). Int J Syst Evol Microbiol 57:2185-2187 (Pubitemid 47497168)
    • (2007) International Journal of Systematic and Evolutionary Microbiology , vol.57 , Issue.9 , pp. 2185-2187
    • Felis, G.E.1    Dellaglio, F.2
  • 17
    • 0026585263 scopus 로고
    • How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity
    • Fox GE, Wisotkey JD, 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    Wisotkey, J.D.2    Jurtshuk Jr., P.3
  • 19
    • 0001901024 scopus 로고    scopus 로고
    • Polyphasic taxonomy
    • Boone DR, Castenholz RW (eds), Garrity GM (editor-in-chief) 2nd edn. The archaea and the deeply branching and phototrophic bacteria. Springer, New York
    • Gillis M, Vandamme P, de Vos P, Swings J, Kersters K (2001) Polyphasic taxonomy. In: Boone DR, Castenholz RW (eds), Garrity GM (editor-in-chief) Bergey's manual of systematic bacteriology, vol 1, 2nd edn. The archaea and the deeply branching and phototrophic bacteria. Springer, New York, pp 43-48
    • (2001) Bergey's Manual of Systematic Bacteriology , vol.1 , pp. 43-48
    • Gillis, M.1    Vandamme, P.2    De Vos, P.3    Swings, J.4    Kersters, K.5
  • 22
    • 33750855471 scopus 로고    scopus 로고
    • Raman microspectroscopy as an identification tool within the phylogenetically homogeneous 'Bacillus subtilis'-group
    • DOI 10.1016/j.syapm.2006.02.001, PII S0723202006000403
    • Hutsebaut D, Vandroemme J, Heyrman J, Dawyndt P, Vandenabeele P, Moens L, de Vos P (2006) Raman microspectroscopy as an identification tool within the phylogenetically homogeneous 'Bacillus subtilis'-group. Syst Appl Microbiol 29:650-660 (Pubitemid 44717524)
    • (2006) Systematic and Applied Microbiology , vol.29 , Issue.8 , pp. 650-660
    • Hutsebaut, D.1    Vandroemme, J.2    Heyrman, J.3    Dawyndt, P.4    Vandenabeele, P.5    Moens, L.6    De Vos, P.7
  • 23
    • 84856219467 scopus 로고    scopus 로고
    • Systematics of prokaryotes: The state of the art
    • Kämpfer P (2012) Systematics of prokaryotes: the state of the art. Antonie van Leeuwenhoek 101:3-11
    • (2012) Antonie Van Leeuwenhoek , vol.101 , pp. 3-11
    • Kämpfer, P.1
  • 24
    • 84856587704 scopus 로고    scopus 로고
    • Prokaryotic taxonomy in the sequencing era - The polyphasic approach revisited
    • Kämpfer P, Glaeser SP (2012) Prokaryotic taxonomy in the sequencing era - the polyphasic approach revisited. Environ Microbiol 14:291-317
    • (2012) Environ Microbiol , vol.14 , pp. 291-317
    • Kämpfer, P.1    Glaeser, S.P.2
  • 27
    • 0000380283 scopus 로고
    • Prospects for a natural system of classification of bacteria
    • Kluyver AJ, van Niel CB (1936) Prospects for a natural system of classification of bacteria. Zentralbl Bakt Parasitenkd II 94:369-403
    • (1936) Zentralbl Bakt Parasitenkd II , vol.94 , pp. 369-403
    • Kluyver, A.J.1    Van Niel, C.B.2
  • 28
    • 14044262978 scopus 로고    scopus 로고
    • Genomic insights that advance the species definition for prokaryotes
    • Konstantinidis K, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102:2567-2592
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 2567-2592
    • Konstantinidis, K.1    Tiedje, J.M.2
  • 29
    • 35748954014 scopus 로고    scopus 로고
    • Prokaryotic taxonomy and phylogeny in the genomic era: Advancements and challenges ahead
    • DOI 10.1016/j.mib.2007.08.006, PII S1369527407001208, Antimicrobials/Genomics
    • Konstantinidis K, Tiedje JM (2007) Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 10:504-509 (Pubitemid 350052687)
    • (2007) Current Opinion in Microbiology , vol.10 , Issue.5 , pp. 504-509
    • Konstantinidis, K.T.1    Tiedje, J.M.2
  • 31
    • 0035910123 scopus 로고    scopus 로고
    • Oceanobacillus iheyensis gen. nov., sp. nov., a deep-sea extremely halotolerant and alkaliphilic species isolated from a depth of 1050 m on the Iheya Ridge
    • DOI 10.1016/S0378-1097(01)00493-1, PII S0378109701004931
    • Lu J, Nogi Y, Takami H (2001) Oceanobacillus iheyensis gen. nov., sp. nov., a deep-sea extremely halotolerant and alkaliphilic species isolated from a depth of 1050 m on the Iheya Ridge. FEMS Microbiol Lett 205:291-297 (Pubitemid 34031935)
    • (2001) FEMS Microbiology Letters , vol.205 , Issue.2 , pp. 291-297
    • Lu, J.1    Nogi, Y.2    Takami, H.3
  • 38
    • 0028082002 scopus 로고
    • Taxonomic notes: A proposal for recording the properties of putative taxa of prokaryotes
    • Murray RGE, Schleifer KH (1994) Taxonomic notes: a proposal for recording the properties of putative taxa of prokaryotes. Int J Syst Bacteriol 44:174-176
    • (1994) Int J Syst Bacteriol , vol.44 , pp. 174-176
    • Murray, R.G.E.1    Schleifer, K.H.2
  • 39
    • 0028887837 scopus 로고
    • Taxonomic note: Implementation of the provisional status candidatus for incompletely described procaryotes
    • Murray RGE, Stackebrandt E (1995) Taxonomic note: implementation of the provisional status candidatus for incompletely described procaryotes. Int J Syst Bacteriol 45:186-187
    • (1995) Int J Syst Bacteriol , vol.45 , pp. 186-187
    • Murray, R.G.E.1    Stackebrandt, E.2
  • 40
    • 1942423770 scopus 로고    scopus 로고
    • Prokaryote diversity and taxonomy: Present status and future challenges
    • Oren A (2004) Prokaryote diversity and taxonomy: present status and future challenges. Phil Trans R Soc B 359:623-638
    • (2004) Phil Trans R Soc B , vol.359 , pp. 623-638
    • Oren, A.1
  • 41
    • 84903943679 scopus 로고    scopus 로고
    • Concepts about phylogeny of microorganisms - An historical overview
    • Oren A, Papke RT (eds) Caister Academic Press, Norfolk
    • Oren A (2010) Concepts about phylogeny of microorganisms - an historical overview. In: Oren A, Papke RT (eds) Molecular phylogeny of microorganisms. Caister Academic Press, Norfolk, pp 1-21
    • (2010) Molecular Phylogeny of Microorganisms , pp. 1-21
    • Oren, A.1
  • 43
    • 83155182872 scopus 로고    scopus 로고
    • How to describe new species of prokaryotes
    • Rainey FA, Oren A (eds) Elsevier, Amsterdam
    • Rainey FA (2011) How to describe new species of prokaryotes. In: Rainey FA, Oren A (eds) Taxonomy of prokaryotes - methods in microbiology, vol 38. Elsevier, Amsterdam, pp 7-14
    • (2011) Taxonomy of Prokaryotes - Methods in Microbiology , vol.38 , pp. 7-14
    • Rainey, F.A.1
  • 44
    • 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 USA 106:19126-19131
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 19126-19131
    • Richter, M.1    Rosselló-Móra, R.2
  • 47
    • 84856571925 scopus 로고    scopus 로고
    • Towards a taxonomy of bacteria and archaea based on interactive and cumulative data repositories
    • Rosselló-Móra R (2012) Towards a taxonomy of bacteria and archaea based on interactive and cumulative data repositories. Environ Microbiol 14:318-334
    • (2012) Environ Microbiol , vol.14 , pp. 318-334
    • Rosselló-Móra, R.1
  • 48
    • 0035174578 scopus 로고    scopus 로고
    • The species concept for prokaryotes
    • DOI 10.1016/S0168-6445(00)00040-1, PII S0168644500000401
    • Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39-67 (Pubitemid 32057196)
    • (2001) FEMS Microbiology Reviews , vol.25 , Issue.1 , pp. 39-67
    • Rossello-Mora, R.1    Amann, R.2
  • 50
    • 20544436001 scopus 로고    scopus 로고
    • The prokaryote - Eukaryote dichotomy: Meanings and mythology
    • Sapp J (2005) The prokaryote - eukaryote dichotomy: meanings and mythology. Microbiol Mol Biol Rev 69:292-305
    • (2005) Microbiol Mol Biol Rev , vol.69 , pp. 292-305
    • Sapp, J.1
  • 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 BM (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 (Pubitemid 24315169)
    • (1994) International Journal of Systematic Bacteriology , vol.44 , Issue.4 , pp. 846-849
    • Stackebrandt, E.1    Goebel, B.M.2
  • 55
    • 0000364659 scopus 로고
    • The main outlines of bacterial classification
    • Stanier RY, van Niel CB (1941) The main outlines of bacterial classification. J Bacteriol 42:437-466
    • (1941) J Bacteriol , vol.42 , pp. 437-466
    • Stanier, R.Y.1    Van Niel, C.B.2
  • 58
    • 84856214874 scopus 로고    scopus 로고
    • Publication of descriptions of novel bacterial taxa in Antonie van Leeuwenhoek
    • Sutcliffe IC, Trujillo ME (2012) Publication of descriptions of novel bacterial taxa in Antonie van Leeuwenhoek. Antonie van Leeuwenhoek 101:13-20
    • (2012) Antonie Van Leeuwenhoek , vol.101 , pp. 13-20
    • Sutcliffe, I.C.1    Trujillo, M.E.2
  • 59
    • 84856214874 scopus 로고    scopus 로고
    • A call to arms for systematists: Revitalizing the purpose and practices underpinning the description of novel microbial taxa
    • Sutcliffe IC, Trujillo ME, Goodfellow M (2012) A call to arms for systematists: revitalizing the purpose and practices underpinning the description of novel microbial taxa. Antonie van Leeuwenhoek 101:13-20
    • (2012) Antonie Van Leeuwenhoek , vol.101 , pp. 13-20
    • Sutcliffe, I.C.1    Trujillo, M.E.2    Goodfellow, M.3
  • 60
    • 0037106449 scopus 로고    scopus 로고
    • Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments
    • Takami H, Takaki Y, Uchiyama I (2002) Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments. Nucleic Acids Res 30:3927-3935
    • (2002) Nucleic Acids Res , vol.30 , pp. 3927-3935
    • Takami, H.1    Takaki, Y.2    Uchiyama, I.3
  • 64
    • 51649217935 scopus 로고
    • Bacillus alcalophilus n. sp.; benevens enkele ervaringen met sterk alcalische voedingsbodems
    • Vedder A (1934) Bacillus alcalophilus n. sp.; benevens enkele ervaringen met sterk alcalische voedingsbodems. Antonie van Leeuwenhoek 1:141-147
    • (1934) Antonie Van Leeuwenhoek , vol.1 , pp. 141-147
    • Vedder, A.1
  • 66
    • 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 ERB (2011) Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology. Syst Appl Microbiol 34:2-11
    • (2011) Syst Appl Microbiol , vol.34 , pp. 2-11
    • Welker, M.1    Moore, E.R.B.2
  • 68
    • 20544466225 scopus 로고
    • Sur la classification des bactéries
    • Winogradsky S (1952) Sur la classification des bactéries. Ann Inst Pasteur 82:125-131
    • (1952) Ann Inst Pasteur , vol.82 , pp. 125-131
    • Winogradsky, S.1
  • 69
    • 0023184331 scopus 로고
    • Bacterial evolution
    • Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221-271
    • (1987) Microbiol Rev , vol.51 , pp. 221-271
    • Woese, C.R.1


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