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Prokaryote Characterization and Identification

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The Prokaryotes

Abstract

Systematics can be defined as the scientific study of organisms with the ultimate goal to characterize and arrange organisms in an orderly manner. Systematics also might be defined as “the study of organismal diversity and interrelationships.” As pointed out already by Cowan (1968), systematics includes taxonomy and aspects of ecology, biochemistry, microscopy, pathology, genetics, and molecular biology.

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References

  • Achtman M, Wagner M (2008) Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 6:431–440

    PubMed  CAS  Google Scholar 

  • Altenburger P, Kämpfer P, Akimov VN, Lubitz W, Busse H-J (1997) Polyamine distribution in actinomycetes with Group B peptidoglycan and species of the genera Brevibacterium, Corynebacterium, and Tsukamurella. Int J Syst Bacteriol 47:270–277

    CAS  Google Scholar 

  • Amann RI, Lin C, Key R, Montgomery L, Stahl DA (1992) Diversity among Fibrobacter isolates: towards a phylogenetic and habitat-based classification. Syst Appl Microbiol 15:23–31

    Google Scholar 

  • Anderson R (1983) Alkylamines: novel lipid constituents in Deinococcus radiodurans. Biochim Biophys Acta 753:266–268

    Google Scholar 

  • Arahal DR, Vreeland RH, Litchfield CD, Mormile MR, Tindall BJ, Oren A, Bejar V, Quesada V, Ventosa A (2007) Recommended minimal standards for describing new taxa of the family Halomonadaceae. Int J Syst Evol Microbiol 57:2436–2446

    PubMed  CAS  Google Scholar 

  • Austin B, Colwell RR (1977) Evaluation of some coefficients for use in numerical taxonomy of microorganisms. Int J Syst Bacteriol 27:204–210

    Google Scholar 

  • Bartual SG, Seifert H, Hippler C, Luzon MA, Wisplinghoff H, Rodriguez-Valera F (2005) Development of a multilocus sequence typing scheme for characterization of clinical isolates of Acinetobacter baumannii. J Clin Microbiol 43:4382–4390

    PubMed  CAS  Google Scholar 

  • Beers RJ, Lockhard WR (1962) Experimental methods in computer taxonomy. J Gen Microbiol 28:633–640

    PubMed  CAS  Google Scholar 

  • Bergey DH, Harrison FC, Breed RS, Hammer BW, Hantoon FM (eds) (1923) Bergey’s manual of determinative bacteriology, 1st edn. Williams and Wilkins, Baltimore

    Google Scholar 

  • Bernardet JF, Nakagawa Y, Holmes B (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Bacteriol 52:1049–1070

    CAS  Google Scholar 

  • Breed RS, Murray EGD, Smith NR (eds) (1957) Bergey’s manual of determinative bacteriology, 7th edn. Williams & Wilkins, Baltimore

    Google Scholar 

  • Brennan PJ (1988) Mycobacterium and other actinomycetes. In: Ratledge C, Wilkinson SG (eds) Microbial lipids, vol 1. Academic, London, pp 203–298

    Google Scholar 

  • Brenner DJ (1973) Deoxyribonucleic acid reassociation in the taxonomy of enteric bacteria. Int J Syst Bacteriol 23:298–307

    CAS  Google Scholar 

  • Brenner DJ, Martin MA, Hoyer BH (1967) Deoxyribonucleic acid homologies among some bacteria. J Bacteriol 94:486–487

    PubMed  CAS  Google Scholar 

  • Brenner DJ, Staley JT, Krieg NR (2001) Classification of prokaryotic organisms and the concept of bacterial speciation. In: Garrity GM (ed) Bergey’s manual of systematic bacteriology, vol 1, 2nd edn. Springer, New York, pp 27–31

    Google Scholar 

  • Brown DR, Whitcomb RF, Bradbury JM (2007) Revised minimal standards for description of new species of the class Mollicutes (division Tenericutes). Int J Syst Evol Microbiol 57:2703–2719

    PubMed  CAS  Google Scholar 

  • Buchanan RE, Gibbons NE (eds) (1974) Bergey’s manual of determinative bacteriology, 8th edn. Williams & Wilkins, Baltimore

    Google Scholar 

  • Busse H-J (2011) Polyamines. In: Rainey F, Oren A (eds) Taxonomy of prokaryotes, vol 38, Methods in microbiology. Elsevier, Amsterdam, pp 15–60

    Google Scholar 

  • Busse H-J, Auling G (1988) Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11:1–8

    CAS  Google Scholar 

  • Busse H-J, Schumann P (1999) Polyamine profiles within genera of the class Actinobacteria with LL-diaminopimelic acid in the peptidoglycan. Int J Syst Bacteriol 49:179–184

    PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Christensen H, Kuhnert P, Busse H-J, Frederiksen WC, Bisgaard M (2007) Proposed minimal standards for the description of genera, species and subspecies of the Pasteurellaceae. Int J Syst Evol Microbiol 57:166–178

    PubMed  CAS  Google Scholar 

  • Chun J, Lee J-H, Jung Y, Kim M, Kim S, Kim BK, Lim Y-W (2007) EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 5:2259–2261

    Google Scholar 

  • Cohn F (1875) Untersuchungen über Bacterien II. Beitr Biol Pflanz 1(3):141–208

    Google Scholar 

  • Cole JR, Konstandinidis K, Farris RJ, Tiedje JM (2010) Microbial diversity and phylogeny: extending from rRNAs to genomes. In: Liu W-T, Jackson JK (eds) Environmental molecular microbiology. Caister Academic Press, Norfolk, pp 1–19

    Google Scholar 

  • Collins MD (1985) Isoprenoid quinone analyses in bacterial classification and identification. In: Goodfellow M, Minnikin DE (eds) Chemical methods in bacterial systematics, vol 20, SAB technical series. Academic, London, pp 267–287

    Google Scholar 

  • Collins MD (1994) Isoprenoid quinones. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 345–401

    Google Scholar 

  • Collins MD, Gilbart J (1983) New members of the coenzyme Q series from the Legionellaceae. FEMS Microbiol Lett 16:251–255

    CAS  Google Scholar 

  • Collins MD, Rodrigues U, Ash C, Aguirre M, Farrow JAE, Martinez-Murcia A, Phillips BA, Williams AM, Wallbanks S (1991) Phylogenetic analysis of the genus Lactobacillus and related lactic acid bacteria as determined by reverse transcriptase sequencing of 16S rRNA. FEMS Microbiol Lett 77:5–12

    CAS  Google Scholar 

  • Colwell RR (1970) Polyphasic taxonomy of bacteria. In: Iizuka H, Hasegawa T (eds) Culture collections of microorganisms. University of Tokyo Press, Tokyo, pp 421–436

    Google Scholar 

  • Cowan ST (1968) A dictionary of microbial taxonomic usage. Oliver & Boyd, Edinburgh

    Google Scholar 

  • Cowan ST (1978) Hill LR (ed) Dictionary of microbial taxonomy. Cambridge University Press, Cambridge

    Google Scholar 

  • Cox AD, Wilkinson SG (1989) Polar lipids and fatty acids of Pseudomonas cepacia. Biochim Biophys Acta 1001:60–67

    PubMed  CAS  Google Scholar 

  • Da Costa MS, Albuquerque L, Nobre MF, Wait R (2011) The extraction and identification of respiratory lipoquinones of prokaryotes and their sue in taxonomy. In: Rainey F, Oren A (eds) Taxonomy of prokaryotes, vol 38, Methods in microbiology. Elsevier, Amsterdam, pp 197–206

    Google Scholar 

  • Dagan T, Artzy-Randrup Y, Martin W (2008) Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci USA 105:10039–10044

    PubMed  CAS  Google Scholar 

  • De Ley J, Park IW, Tijtgat R, van Ermengem J (1966) DNA homology and taxonomy of Pseudomonas and Xanthomonas. Microbiology 42:43–56

    Google Scholar 

  • De Vos P, Trüper HG (2000) Judicial Commission on the International Committee of Systematic Bacteriology. IXth International (IUMS) congress of bacteriology and applied microbiology. Minutes of the meetings, 14, 15, and 18 August 1999, Sydney, Australia. Int J Syst Evol Microbiol 50:2239–2244

    Google Scholar 

  • De Vos P, Trüper HG, Tindall BJ (2005) Judicial Commission of the International Committee on Systematics of Prokaryotes. Xth international (IUMS) congress of bacteriology and applied microbiology. Minutes of the Meetings. Int J Syst Evol Microbiol 55:525–532

    Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Dewhirst FE, Fox JG, On SLW (2000) Recommended minimal standards for describing new species of the genus Helicobacter. Int J Syst Evol Microbiol 50:2231–2237

    PubMed  Google Scholar 

  • Diancourt L, Passet V, Nemec A, Dijkshoorn L, Brisse S (2010) The population structure of Acinetobacter baumannii: expanding multiresistant clones from an ancestral susceptible genetic pool. PLoS One 5:e10034

    PubMed  Google Scholar 

  • Dobson G, Minnikin DE, Minnikin SM, Parlett JH, Goodfellow M (1985) Systematic analysis of complex mycobacterial lipids. In: Goodfellow M, Minnikin DE (eds) Chemical methods in bacterial systematics, vol 20, SAB technical series. Academic, London, pp 237–266

    Google Scholar 

  • Edwards JG (1978) Computer-assisted identification of unknown. In: Sharpe AN, Clark DS (eds) Mechanizing microbiology. Charles C. Thomas, Springfield, pp 280–292

    Google Scholar 

  • Eraso JM, Kaplan S (2009) Regulation of gene expression by PrrA in Rhodobacter sphaeroides 2.4.1: role of polyamines and DNA topology. J Bacteriol 191(13):4341–4352

    PubMed  CAS  Google Scholar 

  • Faller AM, Schleifer KH (1981) Effect of growth phase and oxygen supply on cytochrome composition and morphology of Arthrobacter crystallopoietes. Curr Microbiol 6:253–258

    CAS  Google Scholar 

  • Faller AM, Götz F, Schleifer KH (1980) Cytochrome patterns of staphylococci and micrococci and their taxonomic implications Zentralbl. Bakteriol Mikrobiol Hyg Abt I Orig C1:26–39

    Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Feuerstein BG, Williams LD, Basu HS, Marton LJ (1991) Implications and concepts of polyamine-nucleic acid interactions. J Cell Biochem 46(1):37–47

    PubMed  CAS  Google Scholar 

  • Fischer W (1988) Physiology of lipoteichoic acids in bacteria. Adv Microb Physiol 29:233–302

    PubMed  CAS  Google Scholar 

  • Fox GE, Pechman KR, Woese CR (1977) Comparative cataloging of 16S ribosomal ribonucleic acid: molecular approach to prokaryotic systematics. Int J Syst Bacteriol 27:44–57

    CAS  Google Scholar 

  • Fox GE, Wisotzkey 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

    PubMed  CAS  Google Scholar 

  • Freney J, Kloos WE, Hajek V, Webster JA, Bes M, Brun Y, Vernozy-Rozand C (1999) Recommended minimal standards for description of new staphylococcal species. Int J Syst Bacteriol 49:489–502

    PubMed  CAS  Google Scholar 

  • Fujita Y, Naka N, Doi T, Yano I (2005a) Direct molecular mass determination of trehalose monomycolate from 11 species of mycobacteria by MALDI-TOF mass spectrometry. Microbiology 151:1443–1452

    PubMed  CAS  Google Scholar 

  • Fujita Y, Naka N, McNeil MR, Yano I (2005b) Intact molecular characterization of cord factor (trehalose 6,6′-dimycolate) from nine species of mycobacteria by MALDI-TOF mass spectrometry. Microbiology 151:3403–3416

    PubMed  CAS  Google Scholar 

  • Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ et al (2005) Re-evaluating prokaryotic species. Nat Rev Microbiol 3:733–739

    PubMed  CAS  Google Scholar 

  • Godchaux W, Leadbetter ER (1984) Sulfonolipids of gliding bacteria. Structure of the N-acylaminosulfonates. J Biol Chem 259:2982–2990

    PubMed  CAS  Google Scholar 

  • Goodfellow M (1977) Numerical taxonomy. In: Laskin AI, Lechevalier HA (eds) CRC handbook of microbiology, vol 1, 2nd edn. CRC Press, Cleveland, pp 579–596

    Google Scholar 

  • Goris J, Konstantinidis KT, 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

    PubMed  CAS  Google Scholar 

  • Gram C (1884) Ueber die isolierte Färbung der Schizomyceten in Schnitt- und Trockenpärparaten. Forschitte Med 2:185–189

    Google Scholar 

  • Grimont PAD, Popoff MY, Grimont F, Coynault C, Lemelin M (1980) Reproducibility and correlation study of three deoxyribonucleic acid hybridization procedures. Curr Microbiol 4:325–330

    CAS  Google Scholar 

  • Gyllenberg HG (1965) A model for computer identification of microorganisms. J Gen Microbiol 39:401–405

    PubMed  CAS  Google Scholar 

  • Hamana K, Matsuzaki S (1992) Polyamines as a chemotaxonomic marker in bacterial systematics. Crit Rev Microbiol 18:261–283

    PubMed  CAS  Google Scholar 

  • Hancock IC (1994) Analysis of cell wall constituents of Gram-positive bacteria. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 63–84

    Google Scholar 

  • Hase S, Rietschel ET (1976) Isolation and analysis of the lipid A backbone. Lipid A structure of lipopolysaccharides from various bacterial groups. Eur J Biochem 63:101–107

    PubMed  CAS  Google Scholar 

  • Helander IM, Haikara A (1995) Cellular fatty acyl and alkenyl residues in Megasphaera and Pectinatus species: contrasting profiles and detection of beer spoilage. Microbiol 141:1131–1137

    CAS  Google Scholar 

  • Hill LR (1974) Theoretical aspects of numerical identification. Int J Syst Bacteriol 24:494–499

    Google Scholar 

  • Hirao T, Sato M, Shirahata AY, Kamio Y (2000) Covalent linkage of polyamines to peptidoglycan in Anaerovibrio lipolytica. J Bacteriol 182:1154–1157

    PubMed  CAS  Google Scholar 

  • Holmes B, Hill LR (1985) Computers in diagnostic bacteriology, including identification. In: Goodfellow M, Jones D, Priest FG (eds) Computer assisted bacterial systematics. Academic, London, pp 265–287

    Google Scholar 

  • International Committee on Systematic Bacteriology Subcommittee on the Taxonomy of Mycoplasmatales (1972) Proposal for minimal standards for descriptions of new species of the order Mycoplasmatales. Int J Syst Bacteriol 22:184–188

    Google Scholar 

  • Johnson JL (1973) Use of nucleic-acid homologies in the taxonomy of anaerobic bacteria. Int J Syst Bacteriol 23:308–315

    CAS  Google Scholar 

  • Johnson JL (1984) Nucleic acids in bacterial classification. In: Krieg NR, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 1. Williams & Wilkins, Baltimore, pp 8–11

    Google Scholar 

  • Johnson JL, Ordal EJ (1968) Deoxyribonucleic acid homology in bacterial taxonomy. The effect of incubation temperature and reaction specificity. J Bacteriol 95:893–900

    PubMed  CAS  Google Scholar 

  • Jolley KA, Maiden MC (2010) BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11:595

    PubMed  Google Scholar 

  • Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM et al (2012) Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 158:1005–1015

    PubMed  CAS  Google Scholar 

  • Jones CW, Poole RK (1985) The analysis of cytochromes. In: Gottschalk G (ed) Methods in microbiology, vol 18. Academic, London, pp 285–328

    Google Scholar 

  • Kamio Y, Nakamura K (1987) Putrescine and cadaverine are constituents of peptidoglycan in Veillonella alcalescens and Veillonella parvula. J Bacteriol 169:2881–2884

    PubMed  CAS  Google Scholar 

  • Kamio Y, Itoh Y, Terawaki Y (1981a) Chemical structure of peptidoglycan in Selenomonas ruminantium: cadaverine links covalently to the d-glutamic acid residue of peptidoglycan. J Bacteriol 146:49–53

    PubMed  CAS  Google Scholar 

  • Kamio Y, Itoh Y, Terawaki Y, Kusano T (1981b) Cadaverine is covalently linked to peptidoglycan in Selenomonas ruminantium. J Bacteriol 145:122–128

    PubMed  CAS  Google Scholar 

  • Kämpfer P (2010) The importance of phenotype for bacterial systematics. Bull BISMiS 1(1):7–15

    Google Scholar 

  • Kämpfer P (2012) Systematics of prokaryotes: the state of the art. Antonie Van Leeuwenhoek 101(1):3–11

    PubMed  Google Scholar 

  • Kämpfer P, Glaeser SP (2012) Prokaryotic taxonomy in the sequencing era—the polyphasic approach revisited. Environ Microbiol 14:291–317

    PubMed  Google Scholar 

  • Kandler O, Hippe H (1977) Lack of peptidoglycan in the cell walls of Methanosarcina barkeri. Arch Microbiol 113:57–60

    PubMed  CAS  Google Scholar 

  • Kaneko T (1979) Correlative similarity coefficient: new criterion for forming dendrograms. Int J Syst Bacteriol 29:188–193

    Google Scholar 

  • Karr DE, Bibb WF, Moss CW (1982) Isoprenoid quinones of the genus Legionella. J Clin Microbiol 15:1044–1048

    PubMed  CAS  Google Scholar 

  • Kellogg ST (1979) MICRID: a computer-assisted microbial identification system. Appl Environ Microbiol 38:559–563

    PubMed  CAS  Google Scholar 

  • Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M, Na H et al (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

    PubMed  CAS  Google Scholar 

  • Klenk H-P, Göker M (2010) En route to a genome-based classification of archaea and bacteria? Syst Appl Microbiol 33(4):175–182

    PubMed  CAS  Google Scholar 

  • Koeppel A, Perry EB, Sikorski J, Krizanc D, Warner A, Ward DM et al (2008) Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proc Natl Acad Sci USA 105:2504–2509

    PubMed  CAS  Google Scholar 

  • König H (1994) Analysis of archaeal cell envelopes. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 85–119

    Google Scholar 

  • König H, Kralik R, Kandler O (1982) Structure and modifications of pseudomurein in Methanobacteriales. Zbl Bakt Hyg I Abt Orig C 3:179–191

    Google Scholar 

  • König H, Kandler O, Jensen M, Rietschel ET (1983) The primary structure of the glycan moiety of the pseudomurein from Methanobacterium thermoautotrophicum. Hoppe-Seyler’s Z Physiol Chem 364:627–636

    PubMed  Google Scholar 

  • Konstantinidis KT, Tiedje JM (2005) Genomic insights into the species definition for prokaryotes. Proc Natl Acad Sci USA 102:2567–2572

    PubMed  CAS  Google Scholar 

  • Konstantinidis KT, Ramette A, Tiedje JM (2006) The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 361:1929–1940

    PubMed  Google Scholar 

  • Krieg NR, Padgett PJ (2011) Phenotypic and physiological characterization methods. In: Rainey F, Oren A (eds) Taxonomy of prokaryotes, vol 38, Methods in microbiology. Elsevier, Amsterdam, pp 15–60

    Google Scholar 

  • Kroppenstedt RM, Goodfellow M (1991) The family Thermomonosporaceae. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes, 2nd edn. Springer, New York, pp 1085–1114

    Google Scholar 

  • Kroppenstedt RM, Stackebrandt E, Goodfellow M (1990) Taxonomic revision of the actinomycete genera Actinomadura and Microtetraspora. Syst Appl Microbiol 13:148–160

    CAS  Google Scholar 

  • Labeda DP (2000) International Committee on Systematic Bacteriology. IXth international (IUMS) congress of bacteriology and applied microbiology. Minutes of the meetings, 14 an 17 August 1999, Sydney, Australia. Int J Syst Evol Microbiol 50:2245–2247

    Google Scholar 

  • Langworthy TA, Holzer G, Zeikus JG, Tornabene TG (1983) Iso- and anteiso-branched glycerol diethers of the thermophilic anaerobes Thermodesulfobacterium commune. Syst Appl Microbiol 4:1–17

    PubMed  CAS  Google Scholar 

  • Lapage SP, Bascomb B, Willcox WR, Curtis MA (1970) Computer identification of bacteria. In: Baillie A, Gilbert RJ (eds) Automation, mechanization, and data handling in microbiology. Academic, London, pp 1–22

    Google Scholar 

  • Lapage SP, Bascomb B, Willcox WR, Curtis MA (1973) Identification of bacteria by computer: general aspects and perspectives. J Gen Microbiol 77:273–299

    PubMed  CAS  Google Scholar 

  • Lapage SP, Sneath PHA, Lessel EF, Skerman VBD, Seeliger HPR, Clark WA (1992) International code of nomenclature of bacteria (1990 revision). American Society for Microbiology, Washington, DC

    Google Scholar 

  • Lechevalier MP, Lechevalier H (1970) Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20:435–443

    CAS  Google Scholar 

  • Lévy-Frébault VV, Portaels F (1992) Proposed minimal standards for the genus Mycobacterium and for description of new slowly growing Mycobacterium species. Int J Syst Bacteriol 42:315–323

    PubMed  Google Scholar 

  • Lienau EK, DeSalle R (2009) Evidence, content and corroboration and the tree of life. Acta Biotheor 57:187–199

    PubMed  Google Scholar 

  • Logan NA, Berge O, Bishop AH, Busse H-J, De Vos P, Fritze D, Heyndrickx M, Kämpfer P, Rabinovitch L, Salkinoja-Salonen MS, Seldin L, Ventosa A (2009) Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 59:2114–2121

    PubMed  CAS  Google Scholar 

  • Ludwig W (2010) Molecular phylogeny of microorganisms: is rRNA still a useful marker? In: Oren A, Papke RT (eds) Molecular phylogeny of microorganisms. Caister Academic Press, Norfolk

    Google Scholar 

  • Ludwig W, Klenk H-P (2001) Overview: a phylogenetic backbone and taxonomic framework of prokaryotes. In: Garrity GM (ed) Bergey’s manual of systematic bacteriology, 2nd edn. Springer, New York, pp 49–65

    Google Scholar 

  • Maiden MC, Bygraves JA, Feil E, Morelli G, Russel JE, Urwin R et al (1998) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95:3140–3145

    PubMed  CAS  Google Scholar 

  • Martinez-Murcia AJ, Collins MD (1990) A phylogenetic analysis of the genus Leuconostoc based on reverse transcriptase sequencing of 16S rRNA. FEMS Microbiol Lett 70:73–84

    CAS  Google Scholar 

  • Martinez-Murcia AJ, Benlloch S, Collins MD (1992) Phylogenetic interrelationships of members of the genera Aeromonas and Plesiomonas as determined by 16S ribosomal DNA sequencing: lack of congruence with results of DNA-DNA hybridisations. Int J Syst Bacteriol 42:412–421

    PubMed  CAS  Google Scholar 

  • McCarthy BJ, Bolton ET (1963) An approach to the measurement of genetic relatedness among organisms. Proc Natl Acad Sci USA 50:156–164

    PubMed  CAS  Google Scholar 

  • Miller LT (1982) A single derivatization method for bacterial fatty acid methyl esters including hydroxy acids. J Clin Microbiol 16:584–586

    PubMed  CAS  Google Scholar 

  • Moore ERB, Rosselló-Móra R (2011) MALDI-TOF MS: a return to phenotyping in microbial identification? Syst Appl Microbiol 34:1

    PubMed  Google Scholar 

  • Moore LVH, Bourne DM, Moore WEC (1994) Comparative distribution and taxonomic value of cellular fatty acids in thirty-three genera of anaerobic Gram-negative bacilli. Int J Syst Bacteriol 44:338–347

    PubMed  CAS  Google Scholar 

  • 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

    PubMed  Google Scholar 

  • Müller K-D, Schmid EN, Kroppenstedt RM (1998) Improved identification of mycobacteria by using the microbial identification system in combination with additional trimethylsulfonium hydroxide pyrolysis. J Clin Microbiol 36:2477–2480

    PubMed  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Murray RGE, Stackebrandt E (1995) Taxonomic note: implementation of the provisional status Candidatus for incompletely described prokaryotes. Int J Syst Bacteriol 45:186–187

    PubMed  CAS  Google Scholar 

  • Murray RGE, Brenner DJ, Colwell RR, De Vos P, Goodfellow M, Grimont PAD, Pfennig N, Stackebrandt E, Zavarzin GA (1990) Report of the ad hoc committee on approaches to taxonomy within the Proteobacteria. Int J Syst Bacteriol 40:213–215

    Google Scholar 

  • Naka T, Fujiwaraa N, Yanoc I, Maedaa S, Doed M, Minaminob M, Ikedab N, Katob Y, Watabee K, Kumazawaf Y, Tomiyasug I, Kobayashia K (2003) Structural analysis of sphingophospholipids derived from Sphingobacterium spiritivorum, the type species of genus Sphingobacterium. Biochim Biophys Acta 1635:83–92

    PubMed  CAS  Google Scholar 

  • Neuhaus FC, Baddiley J (2003) A continuum of anionic charge: structures and functions of d-alanyl-teichoic acids in Gram-positive bacteria. Microbiol Mol Biol Rev 67:686–723

    PubMed  CAS  Google Scholar 

  • Oelze J (1985) Analysis of bacteriochlorophylls. In: Gottschalk G (ed) Methods in microbiology, vol 18. Academic, London, pp 257–284

    Google Scholar 

  • Oren A, Ventosa A, Grant WD (1997) Proposed minimal standards for description of new taxa in the order Halobacteriales. Int J Syst Evol Microbiol 47:233–238

    Google Scholar 

  • Ourisson G, Rohmer M, Poralla K (1987) Prokaryotic hopanoides and other polyterpenoidsterol surrogates. Annu Rev Microbiol 41:301–333

    PubMed  CAS  Google Scholar 

  • Pace B, Campbell LL (1971) Homology of ribosomal ribonucleic acid of diverse bacterial species with Escherichia coli and Bacillus stearothermophilus. J Bacteriol 107:543–547

    PubMed  CAS  Google Scholar 

  • Palleroni NJ, Kunisawa R, Contopoulou R, Doudoroff M (1973) Nucleic acid homologies in the genus Pseudomonas. Int J Syst Bacteriol 23:333–339

    CAS  Google Scholar 

  • Peplies J, Kottmann R, Ludwig W, Glöckner F-O (2008) A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes. Syst Appl Microbiol 31:251–257

    PubMed  CAS  Google Scholar 

  • Pfennig N, Wagener S (1986) An improved method of preparing wet mounts for photomicrographs of microorganisms. J Microbiol Methods 4:303–306

    Google Scholar 

  • Rahman O, Dover LG, Sutcliffe IC (2009a) Lipoteichoic acid biosynthesis: two steps forwards, one step sideways? Trends Microbiol 17:219–225

    PubMed  CAS  Google Scholar 

  • Rahman O, Pfitzenmaier M, Pester O, Morath S, Cummings SP, Hartung T, Sutcliffe IC (2009b) Macroamphiphilic components of thermophilic actinomycetes: identification of lipoteichoic acid in Thermobifida fusca. J Bacteriol 191:152–160

    PubMed  CAS  Google Scholar 

  • Rainey FA, Klatte S, Kroppenstedt RM, Stackebrandt E (1995) Dietzia, new genus including Dietzia maris comb. nov., formerly Rhodococcus maris. Int J Syst Bacteriol 45:32–36

    PubMed  CAS  Google Scholar 

  • Rainey FA, Oren A (2012) Taxonomy of prokaryotes – introduction. Methods Microbiol 38:1–5

    Google Scholar 

  • Ratledge C, Wilkinson SG (1988) Microbial lipids, vol 1. Academic, London

    Google Scholar 

  • Rhodes ME (1965) Flagellation as a criterion for the classification of bacteria. Bacteriol Rev 29:442–465

    PubMed  CAS  Google Scholar 

  • Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131

    PubMed  CAS  Google Scholar 

  • Rosselló-Móra R (2006) DNA-DNA reassociation methods applied to microbial taxonomy and their critical evaluation. In: Stackebrandt E (ed) Molecular identification, systematics, and population structure of prokaryotes. Springer, Heidelberg/Berlin, pp 23–50

    Google Scholar 

  • Rosselló-Móra R (2012) Towards a taxonomy of bacteria and archaea based on interactive and cumulative data repositories. Environ Microbiol 14:318–334

    PubMed  Google Scholar 

  • Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67

    PubMed  Google Scholar 

  • Rütters H, Sass H, Cypionka H, Rullkötter J (2001) Monalkylether phospholipids in the sulfate-reducing bacteria Desulfosarcina vaiabilis and Desulforhabdus aminigenus. Arch Microbiol 176:435–442

    PubMed  Google Scholar 

  • Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491

    PubMed  CAS  Google Scholar 

  • Scherer P, Kneifel H (1983) Distribution of polyamines in methanogenic bacteria. J Bacteriol 154:1315–1322

    PubMed  CAS  Google Scholar 

  • Schindler J, Duben J, Lysenko O (1979) Computer-aided numerical identification of Gram-negative fermentative rods on a desk-top computer. J Appl Bacteriol 47:45–51

    PubMed  CAS  Google Scholar 

  • Schleifer K-H (2009) Classification of bacteria and archaea: past, present and future. Syst Appl Microbiol 32:533–542

    PubMed  Google Scholar 

  • Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477

    PubMed  CAS  Google Scholar 

  • Schleifer KH, Ludwig W (1989) Phylogenetic relationships among bacteria. In: Fernholm B, Bremer K, Jörnvall H (eds) The hierarchy of life. Elsevier, Amsterdam, pp 103–117

    Google Scholar 

  • Schleifer KH, Hammes WP, Kandler O (1976) Effect of endogenous and exogenous factors on the primary structures of bacterial peptidoglycan. Adv Microb Physiol 13:245–292

    PubMed  CAS  Google Scholar 

  • Schleifer K-H, Steber J, Mayer H (1982) Chemical composition and structure of the cell wall of Halococcus morrhuae. Zbl Bakt Hyg I Abt Orig C 3:171–178

    CAS  Google Scholar 

  • Schumann P, Kämpfer P, Busse H-J, Evtushenko LI, For the Subcommittee on the Taxonomy of the suborder Micrococcineae of the International Committee on Systematics of Prokaryotes (2009) Proposed minimal standards for describing new genera and species of the suborder Micrococcineae. Int J Syst Bacteriol 59:1823–1849

    CAS  Google Scholar 

  • Shively JM (1974) Inclusion bodies of prokaryotes. Annu Rev Microbiol 28:167–187

    PubMed  CAS  Google Scholar 

  • Simpson GG (1961) Principles of animal taxonomy. Columbia University Press, New York

    Google Scholar 

  • Skerman VBD (1967) A guide to the identification of the genera of bacteria, 2nd edn. Williams & Wilkins, Baltimore

    Google Scholar 

  • Skerman VBD, McGowan V, Sneath PHA (1980) Approved lists of bacterial names. Int J Syst Bacteriol 30:225–420

    Google Scholar 

  • Skerman VDB, McGowan V, Sneath PHA (1989) The approved lists of bacterial names. Int J Syst Bacteriol 30:225–420

    Google Scholar 

  • Sneath PHA (1971) Theoretical aspects of microbiological taxonomy. In: Pérez-Miravete A, Peláez D (eds) Recent advances in microbiology. Asociacióon Mexicana de Microbiología, Mexico City, pp 581–586

    Google Scholar 

  • Sneath PHA (1972) Computer taxonomy. In: Norris JR, Ribbons DW (eds) Methods in microbiology, vol 7A. Academic, London, pp 29–98

    Google Scholar 

  • Sneath PHA (1977) The maintenance of large numbers of strains of microorganisms, and the implications for culture collections. FEMS Microbiol Lett 1:333–334

    Google Scholar 

  • Sneath PHA (1979a) BASIC program for a significance test for two clusters in Euclidian space as measured by their overlap. Comput Geosci 5:143–155

    Google Scholar 

  • Sneath PHA (1979b) BASIC program for identification of an unknown with presence-absence data against an identification matrix of percent positive characters. Comput Geosci 5:195–213

    Google Scholar 

  • Sneath PHA (1979c) BASIC program for character separation indices from an identification matrix of percent positive characters. Comput Geosci 5:349–357

    Google Scholar 

  • Sneath PHA (1980a) BASIC program for the most diagnostic properties of groups from an identification matrix of percent positive characters. Comput Geosci 6:21–26

    Google Scholar 

  • Sneath PHA (1980b) BASIC program for determining the best identification scores possible for the most typical example when compared with an identification matrix of percent positive characters. Comput Geosci 6:27–34

    Google Scholar 

  • Sneath PHA (1980c) BASIC program for determining overlap between groups in an identification matrix of percent positive characters. Comput Geosci 6:267–278

    Google Scholar 

  • Sneath PHA (1989) Analysis and interpretation of sequence data for bacterial systematics—the view of a numerical taxonomist. Syst Appl Microbiol 12:15–31

    Google Scholar 

  • Sneath PHA (2001) Bacterial nomenclature. In: Garrity GM (ed) Bergey’s manual of systematic bacteriology, vol 1, 2nd edn. Springer, New York, pp 83–88

    Google Scholar 

  • Sneath PHA (2005) The preparation of the approved lists of bacterial names. Int J Syst Evol Microbiol 55:2247–2249

    PubMed  CAS  Google Scholar 

  • Sneath PHA, Sokal RR (1973) Numerical taxonomy, the principles and practice of numerical classification. Freeman, San Francisco

    Google Scholar 

  • Sokal RR, Sneath PHA (1963) Numerical taxonomy. Freeman, San Francisco

    Google Scholar 

  • Soria-Carrasco V, Valens-Vadell M, Peña A, Antón J, Amann R, Castresana J, Rosselló-Móra R (2007) Phylogenetic position of Salinibacter ruber based on concatenated protein alignments. Syst Appl Microbiol 30:171–179

    PubMed  CAS  Google Scholar 

  • Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 8:6–9

    Google Scholar 

  • 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

    CAS  Google Scholar 

  • Stackebrandt E, Woese CR (1981) Towards a phylogeny of the Actinomycetes and related organism. Curr Microbiol 5:197–202

    CAS  Google Scholar 

  • Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P, Maiden MCJ et al (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

    PubMed  CAS  Google Scholar 

  • Staehelin LA, Golecki JR, Fuller RC, Drews G (1978) Visualization of the supramolecular architecture of chlorosomes (chlorobium type vesicles) in freeze-fractured cells of Chloroflexus aurantiacus. Arch Microbiol 119:269–277

    Google Scholar 

  • Staley JT, Krieg NR (1984) Classification of prokaryotic organisms: an overview. In: Murray RG, Brenner DJ, Bryant MP, Holt JG, Krieg NR, Moulder JW, Pfennig N, Sneath PHA, Staley JT (eds) Bergey’s manual of systematic bacteriology, vol 1. Williams and Wilkins, Baltimore, pp 1–4

    Google Scholar 

  • Stanier RY, Van Niel CB (1962) The concept of a bacterium. Arch Microbiol 42:7–35

    Google Scholar 

  • Stanier RY, Ingraham JL, Wheelis ML, Paintes PR (1986) The microbial world, 5th edn. Prentice-Hall, Englewood Cliffs

    Google Scholar 

  • Tindall BJ (1999) Misunderstanding the bacteriological code. Int J Syst Bacteriol 49:1313–1316

    PubMed  Google Scholar 

  • Tindall BJ (2005) Respiratory lipoquinones as biomarkers. In: Akkermans A, de Bruijn F, van Elsas D (eds) Molecular microbial ecology manual, 2nd edn. Kluwer, Dordrecht, Section 4.1.5, Supplement 1

    Google Scholar 

  • Tindall BJ (2008) Confirmation of deposit, but confirmation of what? Int J Syst Evol Microbiol 58:1785–1787

    PubMed  CAS  Google Scholar 

  • Tindall BJ, Garrity GM (2008) Proposals to clarify how type strains are deposited and made available to the scientific community for the purpose of systematic research. Int J Syst Evol Microbiol 58:1987–1990

    PubMed  CAS  Google Scholar 

  • Tindall BJ, Kämpfer P, Euzéby JP, Oren A (2006) Valid publication of names of prokaryotes according to the rules of nomenclature: past history and current practice. Int J Syst Evol Microbiol 56:2715–2720

    PubMed  Google Scholar 

  • Tindall BJ, Sikorski J, Smibert RM, Krieg NR (2007) Phenotypic characterization and the principles of comparative systematics. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM, Snyder LR (eds) Methods for general and molecular microbiology. ASM Press, Washington, DC, pp 330–393

    Google Scholar 

  • Tindall BJ, Rosselló-Mora 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

    PubMed  CAS  Google Scholar 

  • Torkko P, Katila M-L, Kontro M (2003) Gas-chromatographic lipid profiles in identification of currently known slowly growing environmental mycobacteria. J Med Microbiol 52:315–323

    PubMed  CAS  Google Scholar 

  • Tornabene TG (1985) Lipid analysis and the relationship to chemotaxonomy. In: Gottschalk G (ed) Methods in microbiology, vol 18. Academic, London, pp 209–234

    Google Scholar 

  • Trüper HG, Euzéby JP (2009) International code of nomenclature of prokaryotes. Appendix 9: orthography. Int J Syst Evol Microbiol 59(Pt 8):2107–2113

    PubMed  Google Scholar 

  • Trüper HG, Schleifer KH (2006) Prokaryote characterization and identification. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes: a handbook on the biology of bacteria, vol 1, 3rd edn. Springer, New York, pp 58–79

    Google Scholar 

  • Ursing J, Rosselló-Mora RA, Garcia-Valdez E, Lalucat J (1995) Taxonomic note: a pragmatic approach to the nomenclature of phenotypically similar genomic groups. Int J Syst Bacteriol 45:604

    Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • 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

    Google Scholar 

  • Weckesser J, Mayer H (1988) Different lipid A types in lipopolysaccharides of phototrophic and related non-phototrophic bacteria. FEMS Microbiol Rev 54:1431–1454

    Google Scholar 

  • Welker M, Moore ER (2011) Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology. Syst Appl Microbiol 34:2–11

    Google Scholar 

  • Willumsen P, Karlson U, Stackebrandt E, Kroppenstedt RM (2001) Mycobacterium frederiksbergense sp. nov., a novel polycyclic aromatic hydrocarbon-degrading Mycobacterium species. Int J Syst Evol Microbiol 51:1715–1722

    PubMed  CAS  Google Scholar 

  • Wisplinghoff H, Hippler C, Bartual SG, Haefs C, Stefanik D, Higgins PG, Seifert H (2008) Molecular epidemiology of clinical Acinetobacter baumannii and Acinetobacter genomic species 13TU isolates using a multilocus sequencing typing scheme. Clin Microbiol Infect 14:708–715

    PubMed  CAS  Google Scholar 

  • Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271

    PubMed  CAS  Google Scholar 

  • Woese CR, Fox G (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088–5090

    PubMed  CAS  Google Scholar 

  • Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposla for the domains: archaea. Bacteria and Eucarya. Proc Natl Acad Sci USA 87:4576–4579

    PubMed  CAS  Google Scholar 

  • Wolf Y, Rogozin I, Grishin N, Tatusov R, Koonin E (2001) Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol 1:8

    PubMed  CAS  Google Scholar 

  • Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rossello-Mora R (2008) The all-species living tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250

    PubMed  CAS  Google Scholar 

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Correspondence to Peter Kämpfer .

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∗The basis of this section has been the excellent short review of Tindall et al. (2007) supplemented with further details given by Tindall et al. (2010)

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Kämpfer, P., Glaeser, S.P. (2013). Prokaryote Characterization and Identification. In: Rosenberg, E., DeLong, E.F., Lory, S., Stackebrandt, E., Thompson, F. (eds) The Prokaryotes. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30194-0_6

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