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Chapter 17 : Taxonomy and Classification of Bacteria

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Abstract:

This chapter discusses the state of the art in bacterial taxonomy. It addresses criteria for species delineation, the polyphasic species concept, and multilocus sequence- and whole-genome sequence-based approaches for species definition. An overview of classification and identification methods is presented, which includes traditional phenotypic, chemotaxonomic, and genotypic techniques. In addition, the chapter briefly describes major groups of bacteria, the practice of reporting the taxonomy of uncultured bacteria, bacterial nomenclature, the valid publication of bacterial names, and name changes.

Citation: Vandamme P. 2015. Taxonomy and Classification of Bacteria, p 255-269. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch17
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References

/content/book/10.1128/9781555817381.mcm11.ch17
1. Cowan ST. 1970. Heretical taxonomy for bacteriologists. J Gen Microbiol 61:145154.
2. Cowan ST. 1965. Principles and practice of bacterial taxonomy—a forward look. J Gen Microbiol 39:143153.
3. Cowan ST. 1971. Sense and nonsense in bacterial taxonomy. J Gen Microbiol 67:18.
4. Gevers D,, Dawyndt P,, Vandamme P,, Willems A,, Vancanneyt M,, Swings J,, De Vos P. 2006. Stepping stones towards a new prokaryotic taxonomy. Philos Trans R Soc Lond B Biol Sci 361:19111916.
5. Richter M,, Rossello-Mora R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106:1912619131.
6. Fraser C,, Alm EJ,, Polz MF,, Spratt BG,, Hanage WP. 2009. The bacterial species challenge: making sense of genetic and ecological diversity. Science 323:741746.
7. Konstantinidis KT,, Ramette A,, Tiedje JM. 2006. The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 361:19291940.
8. Woese CR. 1987. Bacterial evolution. Microbiol Rev 51:221271.
9. Vandamme P,, Pot B,, Gillis M,, de Vos P,, Kersters K,, Swings J. 1996. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407438.
10. Sutcliffe IC,, Trujillo ME,, Goodfellow M. 2012. A call to arms for systematists: revitalising the purpose and practises underpinning the description of novel microbial taxa. Antonie Van Leeuwenhoek 101:1320.
11. Busse HJ,, Denner EB,, Lubitz W. 1996. Classification and identification of bacteria: current approaches to an old problem. Overview of methods used in bacterial systematics. J Biotechnol. 47:338.
12. Wayne LG,, Brenner DJ,, Colwell RR,, Grimont PA,, Kandler P,, Krichevsky MI,, Moore LH,, Moore WE,, Murray RG,, Stackebrandt E,, Starr MP,, Tru¨per HG. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463464.
13. Tindall BJ,, Rossello-Mora R,, Busse HJ,, Ludwig W,, Kampfer P. 2010. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249266.
14. Tindall BJ,, Sikorski J,, Smibert RM,, Krieg NR,. 2007. Phenotypic characterization and the principles of comparative systematics, p 330393. In Reddy CA,, Beveridge TJ,, Breznak JA,, Marzluf G,, Schmidt TM,, Snyder LR (ed), Methods for General and Molecular Microbiology. ASM Press, Washington, DC.
15. Colwell RR. 1970. Polyphasic taxonomy of genus Vibrio—numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacteriol 104:410433.
16. Vancanneyt M,, Vandamme P,, Kersters K. 1995. Differentiation of Bordetella pertussis, B. parapertussis, and B. bronchiseptica by whole-cell protein electrophoresis and fatty acid analysis. Int J Syst Bacteriol 45:843847.
17. Young JM. 2001. Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy. Int J Syst Evol Microbiol 51:945953.
18. Achtman M,, Wagner M. 2008. Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 6:431440.
19. Ludwig W,, Klenk HP,. 2005. Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systematics, p 4965. In Garrity GM,, Brenner DJ,, Krieg NR,, Staley JT (ed), Bergey's Manual of Systematic Bacteriology, 2nd ed, vol 2, part A. Springer-Verlag, New York, NY.
20. Garrity GM,, Holt JG,. 2001. The road map to the manual, p 119166. In Garrity GM,, Boone DR,, Castenholz RW (ed), Bergey's Manual of Systematic Bacteriology, 2nd ed, vol 1. Springer-Verlag, New York, NY.
21. Bhandari V,, Naushad HS,, Gupta RS. 2012. Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution. Front Cell Infect Microbiol 2:98. 10.3389/fcimb.2012.00098.
22. Stackebrandt E,, Frederiksen W,, Garrity GM,, Grimont PA,, Kampfer P,, Maiden MC,, Nesme X,, Rossello-Mora R,, Swings J,, Truper 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 52:10431047.
23. Gevers D,, Cohan FM,, Lawrence JG,, Spratt BG,, Coenye T,, Feil EJ,, Stackebrandt E,, Van de Peer Y,, Vandamme P,, Thompson FL,, Swings J. 2005. Re-evaluating prokaryotic species. Nat Rev Microbiol 3:733739.
24. Godoy D,, Randle G,, Simpson AJ,, Aanensen DM,, Pitt TL,, Kinoshita R,, Spratt BG. 2003. Multilocus sequence typing and evolutionary relationships among the causative agents of melioidosis and glanders, Burkholderia pseudomallei and Burkholderia mallei. J Clin Microbiol 41:20682079.
25. Kotetishvili M,, Kreger A,, Wauters G,, Morris JG,, Sulakvelidze A,, Stine OC. 2005. Multilocus sequence typing for studying genetic relationships among Yersinia species. J Clin Microbiol 43:26742684.
26. Vandamme P,, Moore ERB,, Cnockaert M,, De Brandt E,, Svensson-Stadler L,, Houf K,, Spilker T,, LiPuma JJ. 2013. Achromobacter animicus sp. nov., Achromobacter mucicolens sp. nov., Achromobacter pulmonis sp. nov. and Achromobacter spiritinus sp. nov., from human clinical samples. Syst Appl Microbiol 36:110.
27. Hanage WP,, Fraser C,, Spratt BG. 2006. Sequences, sequence clusters and bacterial species. Philos Trans R Soc Lond B Biol Sci 361:19171927.
28. Larsen MV,, Cosentino S,, Rasmussen S,, Friis C,, Hasman H,, Marvig RL,, Jelsbak L,, Sicheritz-Ponten T,, Ussery DW,, Aarestrup FM,, Lund O. 2012. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50:13551361.
29. Konstantinidis KT,, Tiedje JM. 2005. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 102:25672572.
30. Tettelin H,, Masignani V,, Cieslewicz MJ,, Donati C,, Medini D,, Ward NL,, Angiuoli SV,, Crabtree J,, Jones AL,, Durkin AS,, Deboy RT,, Davidsen TM,, Mora M,, Scarselli M,, Margarit y Ros I,, Peterson JD,, Hauser CR,, Sundaram JP,, Nelson WC,, Madupu R,, Brinkac LM,, Dodson RJ,, Rosovitz MJ,, Sullivan SA,, Daugherty SC,, Haft DH,, Selengut J,, Gwinn ML,, Zhou L,, Zafar N,, Khouri H,, Radune D,, Dimitrov G,, Watkins K,, O'Connor KJ,, Smith S,, Utterback TR,, White O,, Rubens CE,, Grandi G,, Madoff LC,, Kasper DL,, Telford JL,, Wessels MR,, Rappuoli R,, Fraser CM. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome.” Proc Natl Acad Sci U S A 102:1395013955.
31. Lapierrel P,, Gogarten JP. 2009. Estimating the size of the bacterial pan-genome. Trends Genet 25:107110.
32. Dagan T,, Martin W. 2006. The tree of one percent. Genome Biol 7:118. 10.1186/gb-2006–7-10-118.
33. Koonin EV,, Wolf YI. 2012. Evolution of microbes and viruses: a paradigm shift in evolutionary biology? Front Cell Infect Microbiol 2:119. 10.3389/fcimb .2012.00119.
34. Puigbo P,, Wolf YI,, Koonin EV. 2013. Seeing the Tree of Life behind the phylogenetic forest. BMC Biol 11:46. 10.1186/1741-7007-11-46.
35. Santos SR,, Ochman H. 2004. Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol 6:754759.
36. Zeigler DR. 2003. Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53:18931900.
37. Jolley KA,, Bliss CM,, Bennett JS,, Bratcher HB,, Brehony C,, Colles FM,, Wimalarathna H,, Harrison OB,, Sheppard SK,, Cody AJ,, Maiden MC. 2012. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 158:10051015.
38. Yutin N,, Puigbo P,, Koonin EV,, Wolf YI. 2012. Phylogenomics of prokaryotic ribosomal proteins. PLoS One 7:e36972. 10.1371/journal.pone.0036972.
39. Wang Z,, Wu M. 2013. A phylum-level bacterial phylogenetic marker database. Mol Biol Evol 30:12581262.
40. Didelot X,, Maiden MCJ. 2010. Impact of recombination on bacterial evolution. Trends Microbiol 18:315322.
41. Popa O,, Hazkani-Covo E,, Landan G,, Martin W,, Dagan T. 2011. Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res 21:599609.
42. Lerat E,, Daubin V,, Ochman H,, Moran NA. 2005. Evolutionary origins of genomic repertoires in bacteria. PLoS Biol 3:e130. 10.1371/journal.pbio.
43. Lefebure T,, Bitar PD,, Suzuki H,, Stanhope MJ. 2010. Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept. Genome Biol Evol 2:646655.
44. 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 57:8191.
45. Lucena T,, Ruvira MA,, Arahal DR,, Macian MC,, Pujalte MJ. 2012. Vibrio aestivus sp. nov. and Vibrio quintilis sp. nov., related to Marisflavi and Gazogenes clades, respectively. Syst Appl Microbiol 35:427431.
46. Cohan FM. 2002. What are bacterial species? Annu Rev Microbiol 56:457487.
47. Garrity GM,, Oren A. 2012. Response to Gribaldo and Brochier-Armanet: time for order in microbial systematics. Trends Microbiol 20:353354.
48. Cavalier-Smith T. 2002. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol 52:776.
49. Gribaldo S,, Brochier-Armanet C. 2012. Time for order in microbial systematics. Trends Microbiol 20:209210.
50. Williams KP,, Kelly DP. 2013. Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria. Int J Syst Evol Microbiol 63:29012906.
51. Emerson D,, Rentz JA,, Lilburn TG,, Davis RE,, Aldrich H,, Chan C,, Moyer CL. 2007. A novel lineage of Proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities. PLoS One 2:e667. 10.1371/journal.pone.0000667.
52. Murray RG,, Schleifer KH. 1994. Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes. Int J Syst Bacteriol 44:174176.
53. Murray RG,, Stackebrandt E. 1995. Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes. Int J Syst Bacteriol 45:186187.
54. Rondon MR,, August PR,, Bettermann AD,, Brady SF,, Grossman TH,, Liles MR,, Loiacono KA,, Lynch BA,, MacNeil IA,, Minor C,, Tiong CL,, Gilman M,, Osburne MS,, Clardy J,, Handelsman J,, Goodman RM. 2000. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66:25412547.
55. Tyson GW,, Chapman J,, Hugenholtz P,, Allen EE,, Ram RJ,, Richardson PM,, Solovyev VV,, Rubin EM,, Rokhsar DS,, Banfield JF. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:3743.
56. Raghunathan A,, Ferguson HR,, Bornarth CJ,, Song WM,, Driscoll M,, Lasken RS. 2005. Genomic DNA amplification from a single bacterium. Appl Environ Microbiol 71:33423347.
57. Kvist T,, Ahring BK,, Lasken RS,, Westermann P. 2007. Specific single-cell isolation and genomic amplification of uncultured microorganisms. Appl Microbiol Biotechnol 74:926935.
58. Zoetendal EG,, Rajilic-Stojanovic M,, de Vos WM. 2008. High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 57:16051615.
59. Christensen H,, Angen O,, Mutters R,, Olsen JE,, Bisgaard M. 2000. DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA. Int J Syst Evol Microbiol 50:10951102.
60. Ezaki T,, Hashimoto Y,, Yabuuchi E. 1989. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224229.
61. Goris J,, Suzuki K,, De Vos P,, Nakase T,, Kersters K. 1998. Evaluation of a microplate DNA-DNA hybridization method compared with the initial renaturation method. Can J Microbiol 44:11481153.
62. Deloger M,, El Karoui M,, Petit MA. 2009. A genomic distance based on MUM indicates discontinuity between most bacterial species and genera. J Bacteriol 191:9199.
63. Altschul SF,, Madden TL,, Schaffer AA,, Zhang JH,, Zhang Z,, Miller W,, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:33893402.
64. Vandamme P,, Dawyndt P. 2011. Classification and identification of the Burkholderia cepacia complex: past, present and future. Syst Appl Microbiol 34:8795.
65. Konstantinidis KT,, Ramette A,, Tiedje JM. 2006. Toward a more robust assessment of intraspecies diversity, using fewer genetic markers. Appl Environ Microbiol 72:72867293.
66. Vanlaere E,, Baldwin A,, Gevers D,, Henry D,, De Brandt E,, Lipuma JJ,, Mahenthiralingam E,, Speert DP,, Dowson C,, Vandamme P. 2009. Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species, Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov. Int J Syst Evol Microbiol 59:102111.
67. Hoffmann M,, Monday SR,, Allard MW,, Strain EA,, Whittaker P,, Naum M,, McCarthy PJ,, Lopez JV,, Fischer M,, Brown EW. 2012. Vibrio caribbeanicus sp. nov., isolated from the marine sponge Scleritoderma cyanea. Int J Syst Evol Microbiol 62:17361743.
68. Olsen GJ,, Larsen N,, Woese CR. 1991. The ribosomal RNA database project. Nucleic Acids Res 19(Suppl):20172021.
69. Quast C,, Pruesse E,, Yilmaz P,, Gerken J,, Schweer T,, Yarza P,, Peplies J,, Glockner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590D596.
70. Kim OS,, Cho YJ,, Lee K,, Yoon SH,, Kim M,, Na H,, Park SC,, Jeon YS,, Lee JH,, Yi H,, Won S,, Chun J. 2012. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716721.
71. Cole JR,, Wang Q,, Cardenas E,, Fish J,, Chai B,, Farris RJ,, Kulam-Syed-Mohideen AS,, McGarrell DM,, Marsh T,, Garrity GM,, Tiedje JM. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141D145.
72. Dawyndt P,, Vancanneyt M,, De Meyer H,, Swings J. 2005. Knowledge accumulation and resolution of data inconsistencies during the integration of microbial information sources. IEEE Trans Knowl Data Eng 17:11111126.
73. Stackebrandt E,, Goebel BM. 1994. A place for DNA-DNA reassociation and 16S ribosomal RNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846849.
74. Stackebrandt E,, Ebers J. 2006. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 11:152155.
75. Harrington CS,, On SL. 1999. Extensive 16S rRNA gene sequence diversity in Campylobacter hyointestinalis strains: taxonomic and applied implications. Int J Syst Bacteriol 49:11711175.
76. Vandamme P,, Harrington CS,, Jalava K,, On SL. 2000. Misidentifying helicobacters: the Helicobacter cinaedi example. J Clin Microbiol 38:22612266.
77. Janda JM,, Abbott SL. 2007. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol 45:27612764.
78. Woo PC,, Lau SK,, Teng JL,, Tse H,, Yuen KY. 2008. Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin Microbiol Infect 14:908934.
79. Chakravorty S,, Helb D,, Burday M,, Connell N,, Alland D. 2007. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods 69:330339.
80. Yu Z,, Morrison M. 2004. Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis. Appl Environ Microbiol 70:48004806.
81. Liu WT,, Marsh TL,, Cheng H,, Forney LJ. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63:45164522.
82. Muyzer G,, Dewaal EC,, Uitterlinden AG. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S ribosomal RNA. Appl Environ Microbiol 59:695700.
83. Jordan JA,, Jones-Laughner J,, Durso MB. 2009. Utility of pyrosequencing in identifying bacteria directly from positive blood culture bottles. J Clin Microbiol 47:368372.
84. Kolak M,, Karpati F,, Monstein HJ,, Jonasson J. 2003. Molecular typing of the bacterial flora in sputum of cystic fibrosis patients. Int J Med Microbiol 293:309317.
85. Turenne CY,, Witwicki E,, Hoban DJ,, Karlowsky JA,, Kabani AM. 2000. Rapid identification of bacteria from positive blood cultures by fluorescence-based PCR-single-strand conformation polymorphism analysis of the 16S rRNA gene. J Clin Microbiol 38:513520.
86. Yang S,, Ramachandran P,, Rothman R,, Hsieh YH,, Hardick A,, Won H,, Kecojevic A,, Jackman J,, Gaydos C. 2009. Rapid identification of biothreat and other clinically relevant bacterial species by use of universal PCR coupled with high-resolution melting analysis. J Clin Microbiol 47:22522255.
87. Ochi K. 1995. Comparative ribosomal protein sequence analyses of a phylogenetically defined genus, Pseudomonas, and its relatives. Int J Syst Bacteriol 45:268273.
88. Goh SH,, Potter S,, Wood JO,, Hemmingsen SM,, Reynolds RP,, Chow AW. 1996. HSP60 gene sequences as universal targets for microbial species identification: studies with coagulase-negative staphylococci. J Clin Microbiol 34:818823.
89. Khamis A,, Raoult D,, La Scola B. 2004. rpoB gene sequencing for identification of Corynebacterium species. J Clin Microbiol 42:39253931.
90. Eisen JA. 1995. The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J Mol Evol 41:11051123.
91. Gautier AL,, Dubois D,, Escande F,, Avril JL,, Trieu-Cuot P,, Gaillot O. 2005. Rapid and accurate identification of human isolates of Pasteurella and related species by sequencing the sodA gene. J Clin Microbiol 43:23072314.
92. Poyart C,, Quesne G,, Trieu-Cuot P. 2002. Taxonomic dissection of the Streptococcus bovis group by analysis of manganese-dependent superoxide dismutase gene (sodA) sequences: reclassification of ‘Streptococcus infantarius subsp. coli’ as Streptococcus lutetiensis sp. nov. and of Streptococcus bovis biotype II.2 as Streptococcus pasteurianus sp. nov. Int J Syst Evol Microbiol 52:12471255.
93. Schlegel L,, Grimont F,, Ageron E,, Grimont PA,, Bouvet A. 2003. Reappraisal of the taxonomy of the Streptococcus bovis/Streptococcus equinus complex and related species: description of Streptococcus gallolyticus subsp. gallolyticus subsp. nov., S. gallolyticus subsp. macedonicus subsp. nov. and S. gallolyticus subsp. pasteurianus subsp. nov. Int J Syst Evol Microbiol 53:631645.
94. Savelkoul PH,, Aarts HJ,, de Haas J,, Dijkshoorn L,, Duim B,, Otsen M,, Rademaker JL,, Schouls L,, Lenstra JA. 1999. Amplified-fragment length polymorphism analysis: the state of an art. J Clin Microbiol 37:30833091.
95. Janssen P,, Coopman R,, Huys G,, Swings J,, Bleeker M,, Vos P,, Zabeau M,, Kersters K. 1996. Evaluation of the DNA fingerprinting method AFLP as an new tool in bacterial taxonomy. Microbiology 142:18811893.
96. Ishii S,, Sadowsky MJ. 2009. Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution. Environ Microbiol 11:733740.
97. van Belkum A,, Tassios PT,, Dijkshoorn L,, Haeggman S,, Cookson B,, Fry NK,, Fussing V,, Green J,, Feil E,, Gerner-Smidt P,, Brisse S,, Struelens M,, Escmid E. 2007. Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin Microbiol Inf 13:146.
98. Welsh J,, McClelland M. 1992. PCR-amplified length polymorphisms in tRNA intergenic spacers for categorizing staphylococci. Mol Microbiol 6:16731680.
99. Sokal RR,, Sneath PH. 1963. Principles of Numerical Taxonomy. W. H. Freeman and Co, San Francisco, CA.
100. Schumann P,. 2011. Peptidoglycan structure, p 101129. In Rainey F,, Oren A (ed), Methods in Microbiology, vol 38. Taxonomy of Prokaryotes. Academic Press, London, United Kingdom.
101. Fischer W,, Rosel P,, Koch HU. 1981. Effect of alanine ester substitution and other structural features of lipoteichoic acids on their inhibitory activity against autolysins of Staphylococcus aureus. J Bacteriol 146:467475.
102. Welch DF. 1991. Applications of cellular fatty acid analysis. Clin Microbiol Rev 4:422438.
103. Clark AE,, Kaleta EJ,, Arora A,, Wolk DM. 2013. Matrix-assisted laser desorption ionization–time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev 26:547603.
104. Sandrin TR,, Goldstein JE,, Schumaker S. 2013. MALDI TOF MS profiling of bacteria at the strain level: a review. Mass Spectrom Rev 32:188217.
105. Ghyselinck J,, Van Hoorde K,, Hoste B,, Heylen K,, De Vos P. 2011. Evaluation of MALDI-TOF MS as a tool for high-throughput dereplication. J Microbiol Methods 86:327336.
106. Hurst GB,, Weaver K,, Doktycz MJ,, Buchanan MV,, Costello AM,, Lidstrom ME. 1998. MALDI-TOF analysis of polymerase chain reaction products from methanotrophic bacteria. Anal Chem 70:26932698.
107. Taranenko NI,, Hurt R,, Zhou JZ,, Isola NR,, Huang H,, Lee SH,, Chen CH. 2002. Laser desorption mass spectrometry for microbial DNA analysis. J Microbiol Methods 48:101106.
108. von Wintzingerode F,, Bocker S,, Schlotelburg C,, Chiu NH,, Storm N,, Jurinke C,, Cantor CR,, Gobel UB,, van den Boom D. 2002. Base-specific fragmentation of amplified 16S rRNA genes analyzed by mass spectrometry: a tool for rapid bacterial identification. Proc Natl Acad Sci U S A 99:70397044.
109. Lefmann M,, Honisch C,, Bocker S,, Storm N,, von Wintzingerode F,, Schlotelburg C,, Moter A,, van den Boom D,, Gobel UB. 2004. Novel mass spectrometry-based tool for genotypic identification of mycobacteria. J Clin Microbiol 42:339346.
110. Lundquist M,, Caspersen MB,, Wikstrom P,, Forsman M. 2005. Discrimination of Francisella tularensis subspecies using surface enhanced laser desorption ionization mass spectrometry and multivariate data analysis. FEMS Microbiol Lett 243:303310.
111. Schmid O,, Ball G,, Lancashire L,, Culak R,, Shah H. 2005. New approaches to identification of bacterial pathogens by surface enhanced laser desorption/ionization time of flight mass spectrometry in concert with artificial neural networks, with special reference to Neisseria gonorrhoeae. J Med Microbiol 54:12051211.
112. Yang YC,, Yu H,, Xiao DW,, Liu H,, Hu Q,, Huang B,, Liao WJ,, Huang WF. 2009. Rapid identification of Staphylococcus aureus by surface enhanced laser desorption and ionization time of flight mass spectrometry. J Microbiol Methods 77:202206.
113. Baldwin CD,, Howe GB,, Sampath R,, Blyn LB,, Matthews H,, Harpin V,, Hall TA,, Drader JJ,, Hofstadler SA,, Eshoo MW,, Rudnick K,, Studarus K,, Moore D,, Abbott S,, Janda JM,, Whitehouse CA. 2009. Usefulness of multilocus polymerase chain reaction followed by electrospray ionization mass spectrometry to identify a diverse panel of bacterial isolates. Diagn Microbiol Infect Dis 63:403408.
114. Ecker DJ,, Sampath R,, Massire C,, Blyn LB,, Hall TA,, Eshoo MW,, Hofstadler SA. 2008. Ibis T5000: a universal biosensor approach for microbiology. Nat Rev Microbiol 6:553558.
115. Ngo Thi NA,, Kirschner C,, Naumann D,. 2000. FT-IR microspectrometry: a new tool for characterizing micro-organisms, p 3644. In Mahadevan-Jansen A,, Puppels GJ (ed), Biomedical Spectroscopy: Vibrational Spectroscopy and Other Novel Techniques, vol 1. SPIE—International Society for Optical Engineering, Bellingham, WA.
116. Sundaram J,, Park B,, Hinton A,, Yoon SC,, Lawrence KC. 2012. Identification and characterization of Salmonella serotypes using DNA spectral characteristics by Fourier transform infrared. Proc SPIE 8369, Sensing for Agriculture and Food Quality and Safety IV, 83690O. 10.1117/12.918585.
117. Fontoura I,, Belo R,, Sakane K,, Cardoso MA,, Khouri S,, Uehara M,, Raniero L,, Martin AA. 2010. FT-IR microspectroscopy in rapid identification of bacteria in pure and mixed culture. Proc SPIE 7560, Biomedical Vibrational Spectroscopy IV: Advances in Research and Industry, 75600T. 10.1117/12.841918.
119. Nie M,, Zhang WQ,, Xiao M,, Luo JL,, Bao K,, Chen JK,, Li B. 2007. FT-IR spectroscopy and artificial neural network identification of Fusarium species. J Phytopathol 155:364367.
120. Sneath PHA (ed). 1992. International Code of Nomenclature of Bacteria, 1990 revision. American Society for Microbiology, Washington, DC.
121. Skerman VB,, McGowan V,, Sneath PH. 1980. Approved lists of bacterial names. Int J Syst Bacteriol 30:225420.
122. De Vos P,, De Ley J. 1983. Intra- and intergeneric similarities of Pseudomonas and Xanthomonas ribosomal ribonucleic acid cistrons. Int J Syst Bacteriol 33:487509.
123. Kersters K,, Ludwig W,, Vancanneyt M,, DeVos P,, Gillis M,, Schleifer KH. 1996. Recent changes in the classification of the pseudomonads: an overview. Syst Appl Microbiol 19:465477.
124. Yabuuchi E,, Kosako Y,, Oyaizu H,, Yano I,, Hotta H,, Hashimoto Y,, Ezaki T,, Arakawa M. 1992. Proposal of Burkholderia gen. nov.; and transfer of seven species of the Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiol Immunol 36:12511275.
125. Yabuuchi E,, Kosako Y,, Yano I,, Hotta H,, Nishiuchi Y. 1995. Transfer of two Burkholderia and an Alcaligenes species to Ralstonia gen. nov.: proposal of Ralstonia pickettii (Ralston, Palleroni and Doudoroff 1973) comb. nov., Ralstonia solanacearum (Smith 1896) comb. nov. and Ralstonia eutropha (Davis 1969) comb. nov. Microbiol Immunol 39:897904.
126. Suarez-Moreno ZR,, Caballero-Mellado J,, Coutinho BG,, Mendonca-Previato L,, James EK,, Venturi V. 2012. Common features of environmental and potentially beneficial plant-associated Burkholderia. Microb Ecol 63:249266.
127. Estrada-de los Santos P,, Vinuesa P,, Martinez-Aguilar L,, Hirsch AM,, Caballero-Mellado J. 2013. Phylogenetic analysis of Burkholderia species by multilocus sequence analysis. Curr Microbiol 67:5160.
128. Palleroni NJ,, Bradbury JF. 1993. Stenotrophomonas, a new bacterial genus for Xanthomonas maltophilia (Hugh 1980) Swings et al. 1983. Int J Syst Bacteriol 43:606609.
129. Caro-Quintero A,, Konstantinidis KT. 2012. Bacterial species may exist, metagenomics reveal. Environ Microbiol 14:347355.
130. Tamames J,, Rossello-Mora R. 2012. On the fitness of microbial taxonomy. Trends Microbiol 20:514516

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