Then and now: a systematic review of the systematics of prokaryotes in the last 80 years
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Barker HA (1939/1940) Studies upon the methane fermentation. IV. The isolation and culture of Methanobacterium Omelianskii. Antonie van Leeuwenhoek 6:201–210
Bergey DH, Breed RS, Hammer BW, Huntoon FM, Murray EGD, Harrison FC (eds) (1934) Bergey’s manual of determinative bacteriology, 4th edn. Williams and Wilkins, 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
Chatton E (1938) Titre et traveaux scientifique (1906–1937) de Edouard Chatton. Sette, Sottano
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
Coenye T, Gevers D, Van de Peer Y, Vandamme P, Swings J (2005) Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev 29:147–167
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
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
Cowan ST (1962) The microbial species—a macromyth. In: Ainsworth GC, Sneath PHA (eds) Microbial classification. 12th symposium of the society for general microbiology. Cambridge University Press, Cambridge, pp 433–455
Cowan ST (1978) A dictionary of microbial taxonomy. Cambridge University Press, Cambridge
de Graaff WC (1936) Bacterium pneumoniae en Bacterium lactis aerogenes. Antonie van Leeuwenhoek 3:18–27
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
Dobell C (1932) Antony van Leeuwenhoek and his “little animals”. Being some account of the father of protozoology and bacteriology and his multifarious discoveries in these disciplines. N.V. Swets & Zeitlinger, Amsterdam
Dridi PB, Drancourt M (2011) Characterization of prokaryotes using MALDI-TOF mass spectrometry. In: Rainey FA, Oren A (eds) How to describe new species of prokaryotes. Taxonomy of prokaryotes—methods in microbiology, vol 38. Elsevier, Amsterdam, pp 283–297
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
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A (2008) The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 26:541–547
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
Garrity GM, Banfield J, Eisen J, van der Lelie N, McMahon T, Rusch D, DeLong E, Moran MA, Currie C, Fuhrman J, Hallam S, Hugenholtz P, Moran N, Nelson K, Roberts R, Stepanauskas R (2013) Prokaryotic super program advisory committee DOE joint genome institute, Walnut Creek, CA, March 27, 2013. Stand Genom Sci. 8:561–570
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
Goris J, Konstantinidis K, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91
Henrici AT (1939) The biology of bacteria. An introduction to general microbiology, 2nd edn. D.C. Heath & Co, Boston
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
Kämpfer P, Glaeser SP (2012) Prokaryotic taxonomy in the sequencing era—the polyphasic approach revisited. Environ Microbiol 14:291–317
Keswani J, Whitman WB (2001) Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes. Int J Syst Evol Microbiol 51:667–678
Klappenbach JA, Saxman PR, Cole JR, Schmidt TM (2001) rrndb: the Ribosomal RNA operon copy number database. Nucleic Acids Res 29:181–184
Kluyver AJ, van Niel CB (1936) Prospects for a natural system of classification of bacteria. Zentralbl Bakt Parasitenkd II 94:369–403
Konstantinidis K, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102:2567–2592
Konstantinidis K, Tiedje JM (2007) Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 10:504–509
Lapage SP, Sneath PHA, Lessel EF, Skerman VBD, Seeliger HPR, Clark WA (eds) (1992) International code of nomenclature of bacteria (1990 Revision). Bacteriological code. American Society for Microbiology, Washington, DC
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
Marcy Y, Ouverney C, Bik EM, Lösekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz P, Relman DA, Quake SR (2007) Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci USA 104:11889–11894
Meier-Kolthoff JP, Göker M, Spröer C, Klenk H-P (2013) When should a DDH experiment be mandatory in microbial taxonomy? Arch Microbiol 195:413–414
Meisel S, Stöckel S, Elschner M, Melzer F, Rösch P, Popp J (2012) Raman spectroscopy as a potential tool for detection of Brucella spp. in milk. Appl Environ Microbiol 78:5575–5583
Moore ERB, Mihaylova SA, Vandamme P, Krichevsky MI, Dijkshoorn L (2010) Microbial systematics and taxonomy: relevance for a microbial commons. Res Microbiol 161:430–438
Müller OF (1773) Vermium terrestrium et fluviatilium, seu animalium infusoriorum, helminthicorum et testaceorum, non marinorum, succincta historia. Hauniae & Lipsiae
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
Murray RGE, Stackebrandt E (1995) Taxonomic note: implementation of the provisional status candidatus for incompletely described procaryotes. Int J Syst Bacteriol 45:186–187
Oren A (2004) Prokaryote diversity and taxonomy: present status and future challenges. Phil Trans R Soc B 359:623–638
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
Papke RT, Zhaxybayeva O, Fell EJ, Sommerfeld K, Muise D, Doolittle WF (2007) Searching for species in haloarchaea. Proc Natl Acad Sci USA 104:14092–14097
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
Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131
Rinke C, Schwienkek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng J-F, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu W-T, Eisen JA, Hallam SJ, Kyrpides NC, Stapanauskas R, Rubin EM, Hugengoltz P, Woyke T (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature. doi: 10.1038/nature12352
Rösch P, Harz M, Schmitt M, Peschke K-D, Ronneberger O, Burkhardt H, Motzkus H-W, Lankers M, Hofer S, Thiele H, Popp J (2005) Chemotaxonomic identification of single bacteria by micro-Raman spectroscopy: application to clean-room-relevant biological contaminations. Appl Environ Microbiol 71:1626–1637
Rosselló-Móra R (2012) Towards a taxonomy of bacteria and archaea based on interactive and cumulative data repositories. Environ Microbiol 14:318–334
Rosselló-Mora R, Urdiain M, López-López A (2011) DNA–DNA hybridization. In: Rainey FA, Oren A (eds) Taxonomy of prokaryotes—methods in microbiology, vol 38. Elsevier, Amsterdam, pp 325–347
Sapp J (2005) The prokaryote–eukaryote dichotomy: meanings and mythology. Microbiol Mol Biol Rev 69:292–305
Schlegel HG (1999) Geschichte der Mikrobiologie. Acta Historica Leopoldina, Halle
Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155
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
Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P, Maiden MCJ, Nesme X, Rosseló-Mora R, Swings J, Trüper HG, Vauterin L, Ward AC, Whitman WB (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047
Stanier RY, van Niel CB (1941) The main outlines of bacterial classification. J Bacteriol 42:437–466
Stanier RY, Doudoroff M, Adelberg EA (1970) General microbiology, 3rd edn. Macmillan, London
Sutcliffe IC, Trujillo ME (2012) Publication of descriptions of novel bacterial taxa in Antonie van Leeuwenhoek. Antonie van Leeuwenhoek 101:13–20
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
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
Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249–266
Vandamme P, Pot B, Gillis M, De Vos P, Kersters K, Swings J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407–438
Vedder A (1934) Bacillus alcalophilus n. sp.; benevens enkele ervaringen met sterk alcalische voedingsbodems. Antonie van Leeuwenhoek 1:141–147
Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464
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
Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 95:6578–6583
Winogradsky S (1952) Sur la classification des bactéries. Ann Inst Pasteur 82:125–131
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D’haeseleer PD, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng J-F, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce EM, Kyrpides NC, Klenk H-P, Eisen JA (2009) A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature 462:1056–1060