Systematics of prokaryotes: The state of the art

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 101, Issue 1, 2012, Pages 3-11

  Kämpfer, Peter ^a  

^a JUSTUS LIEBIG UNIVERSITY   (Germany)

Author keywords

Polyphasic approach; State of the art; Systematics; Taxonomy

Indexed keywords

MOLECULAR MARKER;

16S RRNA GENE; CONFERENCE PAPER; DNA DNA HYBRIDIZATION; GENE SEQUENCE; MARKER GENE; MOLECULAR PHYLOGENY; MULTILOCUS SEQUENCE TYPING; NOMENCLATURE; NONHUMAN; PHENOTYPE; POPULATION STRUCTURE; PRIORITY JOURNAL; PROKARYOTE; RNA GENE; RNA SEQUENCE; TAXONOMIC RANK; TAXONOMY;

ARCHAEA; BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; CHEMISTRY TECHNIQUES, ANALYTICAL; CLASSIFICATION; CLUSTER ANALYSIS; MICROBIOLOGICAL TECHNIQUES; PHYLOGENY;

PROKARYOTA;

EID: 84856219467     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-011-9660-4     Document Type: Conference Paper

References (54)

1. Bapteste E, Boucher Y (2008) Lateral gene transfer challenges principles of microbial systematics. Trends Microbiol 16:200-207
2. Bapteste E, O'Malley MA, Beiko RG, Ereshefky M, Gogarten JP, Franklin-Hall L et al (2009) Prokaryotic evolution and the tree of life are two different things. Biology Direct 4:34. doi:101186/1745-6150-4-34.
3. 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
4. Brenner S (2010) Sequences and consequences. Phil Trans R Soc B 365:207-212
5. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287 (Pubitemid 43334717)
6. Cole JR, Konstinidis K, Farris RJ, Tiedje JM (2010) Microbial diversity phylogeny: extending from rRNAs to genomes. In: Liu W-T, Jackson JK (eds) Environmental molecular microbiology. Caister Academic Press, Norfolk, pp 1-19
7. 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
8. Cowan ST (1978) A dictionary of microbial taxonomy. Cambridge University Press, Cambridge
9. Dagan T, Artzy-Rrandup Y, Martin W(2008) Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Nat Acad Sci USA 105: 10039-10044
10. De Vos P, Trüper HG (2000) Judicial Commission of the International Committee of Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15, 18 August 1999, Sydney, Australia. Int J Syst Evol Microbiol 50:2239-2244
11. Doroghazi JR, Buckley DH (2010) Widespread homologous recombination within and between Streptomyces species. ISME J 4:136-1143
12. Euzéby JP (1997) List of bacterial names with standing in nomenclature: a folder available on the Internet. Int J Syst Bacteriol 47:590-592 (Pubitemid 27163937)
13. 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 (Pubitemid 41195089)
14. Giffard P (2010) Bioinformatics of microbial sequences. In: Sintchenko V (ed) Infectious diseases informatics. Springer, New York, pp 27-52
15. 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 (Pubitemid 46152735)
16. Harayama S, Kasai H (2006) Bacterial phylogeny reconstruction from molecular sequences. In: Stackebrandt E (ed) Molecular identification, systematics, and population structure of prokaryotes. Springer, Berlin, pp 105-140
17. Kämpfer P (2010) Certificates of deposit-a key element of the bacteriological code and an indispensable prerequisite for comparative taxonomic research. Report of a case of falsification and a reply to the letter to the editor by Tindall (2008). Int J Syst Evol Microbiol 60:475-477
18. Kämpfer P, Glaeser S (2011a) Prokaryotic taxonomy in the sequencing era and the role of MLSA in classification. Microbiology Australia 32:66-70
19. Kämpfer P, Glaeser S. (2011b) Prokaryotic taxonomy in the sequencing era-the polyphasic approach revisited. Env Microbiol (in press)
20. Klenk H-P, Göker M (2010) En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 33:175-182
21. 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 (Pubitemid 44787028)
22. Konstantinidis KT, Tiedje JM (2005) Genomic insights into the species definition for prokaryotes. Proc Natl Acad Sci USA 102:2567-2572 (Pubitemid 40279417)
23. Konstantinidis KT, Tiedje JM (2007) Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 10:504-509 (Pubitemid 350052687)
24. Koonin EV (2003) Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol 1:27-136
25. Krichevsky MI (2011) What is a bacterial species? I will know it when I see it. The Bulletin of BISMiS 2:17-23
26. Kubatko LS, Degnan JH (2007) Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst Biol 56:17-24
27. Labeda DP (2000) International committee on systematic bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14 and 17 August 1999, Sydney, Australia. Int J Syst Evol Microbiol 50:2245-2247
28. 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
29. 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, pp 65-84
30. 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
31. 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 (Pubitemid 28135868)
32. 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
33. Murray RGE, Brenner DJ, Colwell RR, De Vos P, Goodfellow M, Grimont PAD et al (1990) Report of the ad hoc committee on approaches to taxonomy within the Proteobacteria. Int J Syst Bacteriol 40:213-215 (Pubitemid 20143197)
34. Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 45:19126-19131
35. Sneath PHA (1989) Analysis and interpretation of sequence data for bacterial systematics-the view of a numerical taxonomist. Syst Appl Microbiol 12:15-31
36. Sneath PHA (2007) The species concept. Microbiol Today 34:45
37. Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152-155
38. 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 (Pubitemid 34591239)
39. 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)
40. Stackebrandt E, Woese CR (1981) Towards a phylogeny of the actinomycetes and related organism. Curr Microbiol 5: 197-202 (Pubitemid 11038236)
41. Tindall BJ (2008) Confirmation of deposit, but confirmation of what? Int J Syst Evol Microbiol 58:1785-1787
42. Tindall BJ, De Vos P, Trüper HG (2008a) Judicial Commission of the International Committee of Systematics of Prokaryotes. XIth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 23, 24, 27 July 2005, San Francisco, CA, USA. Int J Syst Evol Microbiol 58:1737-1745
43. 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
44. 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 (Pubitemid 44782480)
45. 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
46. Tindall BJ, Sikorski J, Smibert RA, Krieg NL (2008b) Phenotypic characterization and the principles of comparative systematics. In: Garrity GM (ed) Methods for general and molecular microbiology, 3rd Ed. ASM Press, Washington, pp 330-393
47. Vinuesa P (2010) Multilocus sequence analysis and bacterial species phylogeny estimation. In: Oren A, Papke RT (eds) Molecular phylogeny of microorganisms. Caister Academic Press, norfolk, pp 41-64
48. Wayne LG, Brenner DJ, Colwell RR et al (1987) International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463-464
49. Welker M, Moore ER (2011) Applications of whole-cell matrixassisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology. Syst Appl Microbiol 34:2-11
50. Williams D, Andam CP, Gogarten JP (2010) Horizontal gene transfer and the formation of groups of microorganisms. In: Oren A, Papke RT (eds) Molecular phylogeny of microorganisms. Caister Academic Press, Norfolk, pp 167-184
51. Woese CR (1987) Bacterial evolution. Microbiol Rev 51: 221-271 (Pubitemid 17082512)
52. Woese CR, Fox E (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Nat Acad Sci USA 74:5088-5090 (Pubitemid 8241042)
53. Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rosselló-Móra 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
54. Young JM (2001) Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy. Int J Syst Evol Microbiol 51:945-953 (Pubitemid 32499298)