Phylogenetics and systematics

Lactic Acid Bacteria: Biodiversity and Taxonomy

Volumn 9781444333831, Issue , 2014, Pages 31-44

  Vandamme, Peter ^a   De Bruyne, Katrien ^a,b   Pot, Bruno ^c,d  

^a GHENT UNIVERSITY   (Belgium)

^b Applied Maths NV   (Belgium)

^c INSERM U1019   (France)

^d INSERM   (France)

Author keywords

16S rRNA; AFLP; ARDRA; DNA fingerprinting; Housekeeping genes; Multilocus sequence analysis; Phenotypic methods; Phylogeny; Polyphasic taxonomy; Rep PCR; Ribotyping; Species definition

Indexed keywords

BACTERIA; DNA; GENES; LACTIC ACID; PHYLOGENETIC; POLYMERASE CHAIN REACTION; RNA;

16S RRNA; AFLP; ARDRA; DNA FINGERPRINTING; HOUSEKEEPING GENE; MULTILOCUS SEQUENCE ANALYSIS; PHENOTYPIC METHOD; PHYLOGENY; POLYPHASIC; POLYPHASIC TAXONOMY; REP-PCR; RIBOTYPING; SPECIES DEFINITION;

TAXONOMIES;

EID: 84927795023     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781118655252.ch3     Document Type: Chapter

References (104)

1. Amiel, C., Mariey, L., Denis, C., Pichon, P. & Travert, J. (2001) FTIR spectroscopy and taxonomic purpose: Contribution to the classification of lactic acid bacteria. Lait 81: 249-55.
2. Benito,M.J., Serradilla,M.J., Ruiz-Moyano, S.,Martin, A., Perez-Nevado, F.&Cordoba,M.G. (2008) Rapid differentiation of lactic acid bacteria from autochthonous fermentation of Iberian dry-fermented sausages. Meat Sci. 80: 656-61.
3. Bizzini, A. & Greub, G. (2010) Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, a revolution in clinical microbial identification. Clin. Microbiol. Infect. 16: 1614-19.
4. Björkroth, J. & Holzapfel, W. (2003) Genera Leuconostoc, Oenococcus and Weissella. In: Dworkin M. (ed.), The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community. New York, Springer-Verlag, pp. 267-319.
5. Björkroth, K.J., Geisen, R., Schillinger, U. et al. (2000) Characterization of Leuconostoc gasicomitatum sp. nov., associated with spoiled raw tomato-marinated broiler meat strips packaged under modified-atmosphere conditions. Appl. Environ. Microbiol. 66: 3764-72.
6. Björkroth, K.J., Schillinger, U., Geisen, R. et al. (2002) Taxonomic study of Weissella confusa and description of Weissella cibaria sp. nov., detected in food and clinical samples. Int. J. Syst. Evol. Microbiol. 52: 141-8.
7. Bolotin, A.,Wincker, P., Mauger, S. et al. (2001) The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res. 11: 731-53.
8. Booysen, C., Dicks, L.M.T., Meijering, I. & Ackermann, A. (2002) Isolation, identification and changes in the composition of lactic acid bacteria during the malting of two different barley cultivars. Int. J. Food Microbiol. 76: 63-73.
9. Camu, N., Gonzalez, A., DeWinter, T. et al. (2008) Influence of turning and environmental contamination on the dynamics of populations of lactic acid and acetic acid bacteria involved in spontaneous cocoa bean heap fermentation in Ghana. Appl. Environ. Microbiol. 74: 86-98.
10. Chace, N.M., Sgorbati, B. & London, J. (1981) A comparison of the physical and biochemical properties of NAD-dependent glyceraldehyde-3-phosphate dehydrogenases from 3 lactic-acid bacteria. Zbl. Bakt. Mik. Hyg. I C 2: 1-10.
11. Chelo, I.M., Ze-Ze, L. & Tenreiro, R. (2007) Congruence of evolutionary relationships inside the Leuconostoc-Oenococcus-Weissella clade assessed by phylogenetic analysis of the 16S rRNAgene, dnaA, gyrB, rpoC and dnaK. Int. J. Syst. Evol. Microbiol. 57: 276-86.
12. Chun, J., Lee, J.H., Jung, Y. et al. (2007) EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int. J. Syst. Evol. Microbiol. 57: 2259-61.
13. Claesson, M.J., van Sinderen, D. & O'Toole, P.W. (2008) Lactobacillus phylogenomics - towards a reclassification of the genus. Int. J. Syst. Evol. Microbiol. 58: 2945-54.
14. Coenye, T. & Vandamme, P. (2003) Extracting phylogenetic information from whole-genome sequencing projects: the lactic acid bacteria as a test case. Microbiology 149: 3507-17.
15. Coenye, T., Gevers, D., Van de Peer, Y., Vandamme, P. & Swings, J. (2005) Towards a prokaryotic genomic taxonomy. FEMS Microbiol. Rev. 29: 147-67.
16. Cohan, F.M. (2002)What are bacterial species? Annu. Rev. Microbiol. 56: 457-87.
17. Cole, J.R., Wang, Q., Cardenas, E. et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37: D141-D145.
18. Cowan, S.T. (1965) Principles and practice of bacterial taxonomy - a forward look. J. Gen. Microbiol. 39: 143-53.
19. Cowan, S.T. (1970) Heretical taxonomy for bacteriologists. J. Gen. Microbiol. 61: 145-54.
20. Cowan, S.T. (1971) Sense and nonsense in bacterial taxonomy. J. Gen. Microbiol. 67: 1-8.
21. Dalgaard, P., Vancanneyt, M., Vilalta, N.E., Swings, J., Fruekilde, P. & Leisner, J.J. (2003) Identification of lactic acid bacteria from spoilage associations of cooked and brined shrimps stored under modified atmosphere between 0 degrees C and 25 degrees C. J. Appl. Microbiol. 94: 80-9.
22. De Bruyne, K., Schillinger, U., Caroline, L. et al. (2007) Leuconostoc holzapfelii sp. nov., isolated from Ethiopian coffee fermentation and assessment of sequence analysis of housekeeping genes for delineation of Leuconostoc species. Int. J. Syst. Evol. Microbiol. 57: 2952-9.
23. De Bruyne, K., Franz, C.M., Vancanneyt,M. et al. (2008) Pediococcus argentinicus sp. nov. fromArgentinean fermented wheat flour and identification of Pediococcus species by pheS, rpoA and atpA sequence analysis. Int. J. Syst. Evol. Microbiol. 58: 2909-16.
24. De Bruyne, K., Camu, N., De Vuyst, L. & Vandamme, P. (2010) Weissella fabaria sp. nov., from a Ghanaian cocoa fermentation. Int. J. Syst. Evol. Microbiol. 60: 1999-2005.
25. De Bruyne, K., Slabbinck, B., Waegeman, W., Vauterin, P., De Baets, B. & Vandamme, P. (2011) Bacterial species identification from MALDI-TOF spectra through data analysis and machine learning. Syst. Appl. Microbiol. 34: 20-9.
26. Dellaglio, F., Felis, G.E. & Torriani, S. (2002) The status of the species Lactobacillus casei (Orla-Jensen 1916) Hansen and Lessel 1971 and Lactobacillus paracasei Collins et al. 1989. Request for an Opinion. Int. J. Syst. Evol. Microbiol. 52: 285-7.
27. Deloger,M., El Karoui, M.&Petit,M.A. (2009)Agenomic distance based onMUMindicates discontinuity between most bacterial species and genera. J. Bacteriol. 191: 91-9.
28. den Bakker, H.C., Didelot, X., Fortes, E.D., Nightingale, K.K. & Wiedmann, M. (2008) Lineage specific recombination rates and microevolution in Listeria monocytogenes. BMC Evol. Biol. 8: 277.
29. Drancourt, M., Roux, V., Fournier, P.E.&Raoult,D. (2004) rpoB gene sequence-based identification of aerobic gram-positive cocci of the genera Streptococcus, Enterococcus, Gemella, Abiotrophia, and Granulicatella. J. Clin. Microbiol. 42: 497-504.
30. Ehrmann, M.A., Preissler, P., Danne, M. & Vogel, R.F. (2010) Lactobacillus paucivorans sp. nov., isolated from a brewery environment. Int. J. Syst. Evol. Microbiol. 60: 2353-7.
31. Endo, A. & Okada, S. (2008) Reclassification of the genus Leuconostoc and proposals of Fructobacillus fructosus gen. nov., comb. nov., Fructobacillus durionis comb. nov., Fructobacillus ficulneus comb. nov. and Fructobacillus pseudoficulneus comb. nov. Int. J. Syst. Evol. Microbiol. 58: 2195-205.
32. Endo, A., Okada, S. & Morita, H. (2007) Molecular profiling of Lactobacillus, Streptococcus, and Bifidobacterium species in feces of active racehorses. J. Gen. Appl. Microbiol. 53: 191-200.
33. Felis,G.E., Dellaglio, F., Mizzi, L.&Torriani, S. (2001)Comparative sequence analysis of a recA gene fragment brings new evidence for a change in the taxonomy of the Lactobacillus casei group. Int. J. Syst. Evol. Microbiol. 51: 2113-17.
34. Fraser, C., Alm, E.J., Polz, M.F., Spratt, B.G. & Hanage, W.P. (2009) The bacterial species challenge: making sense of genetic and ecological diversity. Science 323: 741-6.
35. Friedrichs, C., Rodloff, A.C., Chhatwal, G.S., Schellenberger,W. & Eschrich, K. (2007) Rapid identification of viridans streptococci by mass spectrometric discrimination. J. Clin. Microbiol. 45: 2392-7.
36. Gasser, F. (1970) Electrophoretic characterization of lactic dehydrogenases in the genus Lactobacillus. J. Gen. Microbiol. 62: 223-39.
37. Gevers, D., Huys, G. & Swings, J. (2001) Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol. Lett. 205: 31-6.
38. Gevers, D., Cohan, F.M., Lawrence, J.G. et al. (2005) Opinion: Re-evaluating prokaryotic species. Nat. Rev. Microbiol. 3: 733-9.
39. Giraffa,G.,DeVecchi, P.&Rossetti, L. (1998) Note: Identification of Lactobacillus delbrueckii subspecies bulgaricus and subspecies lactis dairy isolates by amplified rDNA restriction analysis. J. Appl. Microbiol. 85: 918-24.
40. Goh, S.H., Facklam, R.R., Chang, M. et al. (2000) Identification of Enterococcus species and phenotypically similar Lactococcus and Vagococcus species by reverse checkerboard hybridization to chaperonin 60 gene sequences. J. Clin.Microbiol. 38: 3953-9.
41. Goris, J., Konstantinidis, K.T., Klappenbach, J.A., Coenye, T., Vandamme, P.&Tiedje, J.M. (2007)DNA-DNAhybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57: 81-91.
42. Groisillier, A. & Lonvaud-Funel, A. (1999) Comparison of partial malolactic enzyme gene sequences for phylogenetic analysis of some lactic acid bacteria species and relationships with the malic enzyme. Int. J. Syst. Bacteriol. 49: 1417-28.
43. Haas, E.S., Banta, A.B., Harris, J.K., Pace, N.R. & Brown, J.W. (1996) Structure and evolution of ribonuclease P RNA in grampositive bacteria. Nucleic Acids Res. 24: 4775-82.
44. Hammes, W.P. & Hertel, C. (2009) Genus I. Lactobacillus Beijerinck 1901, 212AL. In: De Vos, P., Garrity, G.M., Jones, D. et al. (eds), Bergey's Manual of Systematic Bacteriology, Vol. 3: The Firmicutes. Springer, pp. 465-511.
45. Hammes,W.P. & Vogel, R.F. (1995) The genus Lactobacillus. In:Wood, B.J.B. & Holzapfel,W.H. (eds), The Genera of Lactic Acid Bacteria. London: Blackie Academic & Professional, pp. 19-54.
46. Hammes, W.P., Weiss, N. & Holzapfel, W.P. (1991) The genera Lactobacillus and Carnobacterium. In: Balows, A., Trüper, H.G., Dworkin, M., Harder, W. & Schleifer, K.H. (eds), The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology, Isolation Identification, Applications. New York: Springer, pp. 1535-94.
47. Hanage, W.P., Fraser, C. & Spratt, B.G. (2006) Sequences, sequence clusters and bacterial species. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361: 1917-27.
48. Holzapfel, W.H., Haberer, P., Geisen, R., Björkroth, J. & Schillinger, U. (2001) Taxonomy and important features of probiotic microorganisms in food and nutrition.Am. J. Clin. Nutr. 73: 365S-373S.
49. Holzapfel, W.H., Franz, C.M.A.P., Ludwig, W. & Dicks, L.M.T. (2009) Genus III. Pediococcus Claussen 1903, 68AL. In: De Vos, P., Garrity, G.M., Jones, D. et al. (eds), Bergey's Manual of Systematic Bacteriology, Vol. 3: The Firmicutes. Springer, pp. 513-32.
50. Hung, W.C., Tsai, J.C., Hsueh, P.R., Chia, J.S. & Teng, L.J. (2005) Species identification of mutans streptococci by groESL gene sequence. J. Med. Microbiol. 54: 857-62.
51. Janssen, P., Coopman, R., Huys, G. et al. (1996) Evaluation of the DNA fingerprinting method AFLP as a new tool in bacterial taxonomy. Microbiology 142: 1881-93.
52. Ke, D.B., Boissinot, M., Huletsky, A. et al. (2000) Evidence for horizontal gene transfer in evolution of elongation factor Tu in enterococci. J. Bacteriol. 182: 6913-20.
53. Konstantinidis, K.T. & Tiedje, J.M. (2005) Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. USA 102: 2567-72.
54. Konstantinidis, K.T., Ramette, A. & Tiedje, J.M. (2006) Toward a more robust assessment of intraspecies diversity, using fewer genetic markers. Appl. Environ. Microbiol. 72: 7286-93.
55. Kostinek, M., Pukall, R., Rooney, A.P. et al. (2005) Lactobacillus arizonensis is a later heterotypic synonym of Lactobacillus plantarum. Int. J. Syst. Evol. Microbiol. 55: 2485-9.
56. Kunene, N.F., Geornaras, I., von Holy, A. & Hastings, J.W. (2000) Characterization and determination of origin of lactic acid bacteria from a sorghum-based fermented weaning food by analysis of soluble proteins and amplified fragment length polymorphism fingerprinting. Appl. Environ. Microbiol. 66: 1084-92.
57. Lancefield, R.C. (1933) A serological differentiation of human and other groups of hemolytic streptococci. J. Exp.Med. 59: 571-95.
58. Laursen, B.G., Bay, L., Cleenwerck, I. et al. (2005) Carnobacterium divergens and Carnobacterium maltaromaticum as spoilers or protective cultures in meat and seafood: phenotypic and genotypic characterization. Syst. Appl. Microbiol. 28: 151-64.
59. Lefebure, T. & Stanhope, M.J. (2007) Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol. 8: R71.
60. London, J. & Chace, N.M. (1976) Aldolases of lactic-acid bacteria - demonstration of immunological relationships among 8 genera of gram-positive bacteria using an anti-pediococcal aldolase serum. Arch. Microbiol. 110: 121-8.
61. London, J. & Chace, N.M. (1983) Relationships among lactic-acid bacteria demonstrated with glyceraldehyde-3-phosphate dehydrogenase as an evolutionary probe. Int. J. Syst. Bacteriol. 33: 723-37.
62. Ludwig,W. (2007) Nucleic acid techniques in bacterial systematics and identification. Int. J. Food Microbiol. 120: 225-36.
63. Ludwig, W. & Klenk, H.P. (2005) Overview: a phylogenetic backbone and taxonomic framework for Prokaryotic systematics. In: Garrity,G.M., Bean,D.J., Krieg N.R.&Staley, J.T. (eds), Bergey's Manual of Systematic Bacteriology, The Proteobacteria. Part A Introductory Essays vol. 2. Springer, pp. 49-65.
64. Mellmann, A., Cloud, J., Maier, T. et al. (2008) Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in comparison to 16S rRNA gene sequencing for species identification of nonfermenting bacteria. J. Clin. Microbiol. 46: 1946-54.
65. Mori, S., Mori, K., Suzuki, I. & Kasumi, T. (2004) Phylogenetic analysis of Lactococcus lactis subspecies based on decoding the sequence of the pepT tripeptidase gene, the pepV dipeptidase gene and 16S rRNA. Syst. Appl. Microbiol. 27: 414-22.
66. Morse, R., Collins, M.D., Ohanlon, K., Wallbanks, S. & Richardson, P.T. (1996) Analysis of the beta' subunit of DNA-dependent RNApolymerase does not support the hypothesis inferred from16S rRNAanalysis thatOenococcus oeni (formerly Leuconostoc oenos) is a tachytelic (fast-evolving) bacterium. Int. J. Syst. Bacteriol. 46: 1004-9.
67. Moschetti, G., Blaiotta, G., Aponte, M., Mauriello, G., Villani, F. & Coppola, S. (1997) Genotyping of Lactobacillus delbrueckii subsp. bulgaricus and determination of the number and forms of rrn operons in L. delbrueckii and its subspecies. Res. Microbiol. 148: 501-10.
68. Naser, S., Thompson, F.L., Hoste, B. et al. (2005a) Phylogeny and identification of enterococci by atpA gene sequence analysis. J. Clin. Microbiol. 43: 2224-30.
69. Naser, S.M., Thompson, F.L., Hoste, B. et al. (2005b) Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes. Microbiology 151: 2141-50.
70. Naser, S.M., Dawyndt, P., Hoste, B. et al. (2007) Identification of lactobacilli by pheS and rpoA gene sequence analyses. Int. J. Syst. Evol. Microbiol. 57: 2777-89.
71. Olsen, G.J., Larsen, N. & Woese, C.R. (1991) The ribosomal RNA database project. Nucleic Acids Res. 19(Suppl.): 2017-21.
72. Piraino, P., Ricciardi, A., Salzano, G., Zotta, T. & Parente, E. (2006) Use of unsupervised and supervised artificial neural networks for the identification of lactic acid bacteria on the basis of SDS-PAGE patterns of whole cell proteins. J. Microbiol. Meth. 66: 336-46.
73. Pot, B., Hertel, C., Ludwig, W., Descheemaeker, P., Kersters, K. & Schleifer, K.H. (1993) Identification and classification of Lactobacillus acidophilus, L. gasseri and L. johnsonii strains by SDS-PAGE and ribosomal RNA-targeted oligonucleotide probe hybridization. J. Gen. Microbiol. 139: 513-17.
74. Poyart, C., Quesnes, G. & Trieu-Cuot, P. (2000) Sequencing the gene encoding manganese-dependent superoxide dismutase for rapid species identification of enterococci. J. Clin. Microbiol. 38: 415-18.
75. Poyart, C., Quesne, G. & Trieu-Cuot, P. (2002) Taxonomic dissection of the Streptococcus bovis group by analysis of manganesedependent 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: 1247-55.
76. Rademaker, J.L.W.,Herbet, H., Starrenburg, M.J.C. et al. (2007) Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting. Appl. Environ. Microbiol. 73: 7128-37.
77. Ricciardi, A., Parente, E., Piraino, P., Paraggio, M. & Romano, P. (2005) Phenotypic characterization of lactic acid bacteria from sourdoughs for Altamura bread produced in Apulia (Southern Italy). Int. J. Food Microbiol. 98: 63-72.
78. Richter, M. & Rossello-Mora, R. (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106: 19126-31.
79. Rodas, A.M., Ferrer, S. & Pardo, I. (2003) 16S-ARDRA, a tool for identification of lactic acid bacteria isolated from grape must and wine. Syst. Appl. Microbiol. 26: 412-22.
80. Rossetti, L. & Giraffa, G. (2005) Rapid identification of dairy lactic acid bacteria by M13-generated, RAPD-PCR fingerprint databases. J. Microbiol. Meth. 63: 135-44.
81. Scheirlinck, I., Van der Meulen, R., Van Schoor, A. et al. (2008) Taxonomic structure and stability of the bacterial community in Belgian sourdough ecosystems as assessed by culture and population fingerprinting. Appl. Environ. Microbiol. 74: 2414-23.
82. Scheirlinck, I., Van der Meulen, R., De Vuyst, L., Vandamme, P.&Huys,G. (2009) Molecular source tracking of predominant lactic acid bacteria in traditional Belgian sourdoughs and their production environments. J. Appl. Microbiol. 106: 1081-92.
83. Schlegel, L., Grimont, F., Collins, M.D., Regnault, B., Grimont, P.A.D. & Bouvet, A. (2000) Streptococcus infantarius sp. nov., Streptococcus infantarius subsp. infantarius subsp. nov. and Streptococcus infantarius subsp. coli subsp nov., isolated from humans and food. Int. J. Syst. Evol. Microbiol. 50: 1425-34.
84. Schlegel, L., Grimont, F., Ageron, E., Grimont, P.A.D. & 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: 631-45.
85. Schleifer, K.H. & Stackebrandt, E. (1983) Molecular systematics of prokaryotes. Annu. Rev. Microbiol. 37: 143-87.
86. Schleifer, K.H., Kraus, J.,Dvorak, C.,Kilpperbalz, R., Collins, M.D.&Fischer,W. (1985) Transfer of Streptococcus lactis and related streptococci to the genus Lactococcus gen. nov. Syst. Appl. Microbiol. 6: 183-95.
87. Sievers, M., Uermosi, C., Fehlmann, M. & Krieger, S. (2003) Cloning, sequence analysis and expression of the F1F0-ATPase betasubunit from wine lactic acid bacteria. Syst. Appl. Microbiol. 26: 350-6.
88. Stackebrandt, E., Frederiksen, W., Garrity, G.M. 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: 1043-7.
89. Suzuki, K., Funahashi, W., Koyanagi, M. & Yamashita, H. (2004) Lactobacillus paracollinoides sp. nov., isolated from brewery environments. Int. J. Syst. Evol. Microbiol. 54: 115-17.
90. Tanigawa, K., Kawabata, H. &Watanabe, K. (2010) Identification and typing of Lactococcus lactis by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl. Environ. Microbiol. 76: 4055-62.
91. Tapp, J., Thollesson, M. & Herrmann, B. (2003) Phylogenetic relationships and genotyping of the genus Streptococcus by sequence determination of the RNase P RNA gene, rnpB. Int. J. Syst. Evol. Microbiol. 53: 1861-71.
92. Torriani, S., Zapparoli, G. & Dellaglio, F. (1999) Use of PCR-based methods for rapid differentiation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis. Appl. Environ. Microbiol. 65: 4351-6.
93. Torriani, S., Felis, G.E. & Dellaglio, F. (2001) Differentiation of Lactobacillus plantarum, L. pentosus, and L. paraplantarum by recA gene sequence analysis and multiplex PCR assay with recA gene-derived primers. Appl. Environ. Microbiol. 67: 3450-54.
94. Tsai, J.C.,Hsueh, P.R., Lin, H.M., Chang,H.J., Ho, S.W.&Teng, L.J. (2005) Identification of clinically relevant Enterococcus species by direct sequencing of groES and spacer region. J. Clin. Microbiol. 43: 235-41.
95. Ueda, K., Seki, T., Kudo, T., Yoshida, T. & Kataoka, M. (1999) Two distinct mechanisms cause heterogeneity of 16S rRNA. J. Bacteriol. 181: 78-82.
96. van Belkum, A., Tassios, P.T., Dijkshoorn, L. et al. (2007) Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin. Microbiol. Infect. 13: 1-46.
97. 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: 407-38.
98. Van Hoorde, K., Verstraete, T., Vandamme, P. & Huys, G. (2008) Diversity of lactic acid bacteria in two Flemish artisan raw milk Gouda-type cheeses. Food Microbiol. 25: 929-35.
99. Ventura, M., Elli, M., Reniero, R. & Zink, R. (2001) Molecular microbial analysis of Bifidobacterium isolates from different environments by the species-specific amplified ribosomal DNA restriction analysis (ARDRA). FEMS Microbiol. Ecol. 36: 113-21.
100. Ventura, M., Canchaya, C., Meylan, V., Klaenhammer, T.R. & Zink, R. (2003) Analysis, characterization, and loci of the tuf genes in Lactobacillus and Bifidobacterium species and their direct application for species identification. Appl. Environ. Microbiol. 69: 6908-22.
101. Wayne, L.G., Brenner, D.J., Colwell, R.R. et al. (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37: 463-4.
102. Woese, C.R. (1987) Bacterial evolution. Microbiol. Rev. 51: 221-71.
103. Yarza, P., Richter, M., Peplies, J. et al. (2008) The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst. Appl. Microbiol. 31: 241-50.
104. Zeigler, D.R. (2003) Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int. J. Syst. Evol. Microbiol. 53: 1893-900.