Polyphasic taxonomy, a consensus approach to bacterial systematics (original) (raw)

Abstract

Over the last 25 years, a much broader range of taxonomic studies of bacteria has gradually replaced the former reliance upon morphological, physiological, and biochemical characterization. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them in a consensus type of classification, framed in a general phylogeny derived from 16S rRNA sequence analysis. In some cases, the consensus classification is a compromise containing a minimum of contradictions. It is thought that the more parameters that will become available in the future, the more polyphasic classification will gain stability. In this review, the practice of polyphasic taxonomy is discussed for four groups of bacteria chosen for their relevance, complexity, or both: the genera Xanthomonas and Campylobacter, the lactic acid bacteria, and the family Comamonadaceae. An evaluation of our present insights, the conclusions derived from it, and the perspectives of polyphasic taxonomy are discussed, emphasizing the keystone role of the species. Taxonomists did not succeed in standardizing species delimitation by using percent DNA hybridization values. Together with the absence of another "gold standard" for species definition, this has an enormous repercussion on bacterial taxonomy. This problem is faced in polyphasic taxonomy, which does not depend on a theory, a hypothesis, or a set of rules, presenting a pragmatic approach to a consensus type of taxonomy, integrating all available data maximally. In the future, polyphasic taxonomy will have to cope with (i) enormous amounts of data, (ii) large numbers of strains, and (iii) data fusion (data aggregation), which will demand efficient and centralized data storage. In the future, taxonomic studies will require collaborative efforts by specialized laboratories even more than now is the case. Whether these future developments will guarantee a more stable consensus classification remains an open question.

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Selected References

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  1. Aislabie J., Richards N. K., Lyttle T. C. Description of bacteria able to degrade isoquinoline in pure culture. Can J Microbiol. 1994 Jul;40(7):555–560. doi: 10.1139/m94-089. [DOI] [PubMed] [Google Scholar]
  2. Alderton M. R., Korolik V., Coloe P. J., Dewhirst F. E., Paster B. J. Campylobacter hyoilei sp. nov., associated with porcine proliferative enteritis. Int J Syst Bacteriol. 1995 Jan;45(1):61–66. doi: 10.1099/00207713-45-1-61. [DOI] [PubMed] [Google Scholar]
  3. Amann R. I., Ludwig W., Schleifer K. H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev. 1995 Mar;59(1):143–169. doi: 10.1128/mr.59.1.143-169.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Arber W. Evolution of prokaryotic genomes. Gene. 1993 Dec 15;135(1-2):49–56. doi: 10.1016/0378-1119(93)90048-8. [DOI] [PubMed] [Google Scholar]
  5. Archibald A. R., Baddiley J. The teichoic acids. Adv Carbohydr Chem Biochem. 1966;21:323–375. doi: 10.1016/s0096-5332(08)60320-3. [DOI] [PubMed] [Google Scholar]
  6. BAUTZ E. K., BAUTZ F. A. THE INFLUENCE OF NONCOMPLEMENTARY BASES ON THE STABILITY OF ORDERED POLYNUCLEOTIDES. Proc Natl Acad Sci U S A. 1964 Dec;52:1476–1481. doi: 10.1073/pnas.52.6.1476. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Barreau C., Wagener G. Characterization of Leuconostoc lactis strains from human sources. J Clin Microbiol. 1990 Aug;28(8):1728–1733. doi: 10.1128/jcm.28.8.1728-1733.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Bascomb S., Lapage S. P., Curtis M. A., Willcox W. R. Identification of bacteria by computer: identification of reference strains. J Gen Microbiol. 1973 Aug;77(2):291–315. doi: 10.1099/00221287-77-2-291. [DOI] [PubMed] [Google Scholar]
  9. Bastyns K., Chapelle S., Vandamme P., Goossens H., De Wachter R. Specific detection of Campylobacter concisus by PCR amplification of 23S rDNA areas. Mol Cell Probes. 1995 Aug;9(4):247–250. doi: 10.1016/s0890-8508(95)90114-0. [DOI] [PubMed] [Google Scholar]
  10. Belland R. J., Trust T. J. Deoxyribonucleic acid sequence relatedness between thermophilic members of the genus Campylobacter. J Gen Microbiol. 1982 Nov;128(11):2515–2522. doi: 10.1099/00221287-128-11-2515. [DOI] [PubMed] [Google Scholar]
  11. Bingen E. H., Denamur E., Elion J. Use of ribotyping in epidemiological surveillance of nosocomial outbreaks. Clin Microbiol Rev. 1994 Jul;7(3):311–327. doi: 10.1128/cmr.7.3.311. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Blaser M. J., Moss C. W., Weaver R. E. Cellular fatty acid composition of Campylobacter fetus. J Clin Microbiol. 1980 May;11(5):448–451. doi: 10.1128/jcm.11.5.448-451.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Bowman J. P., Sly L. I., Hayward A. C., Spiegel Y., Stackebrandt E. Telluria mixta (Pseudomonas mixta Bowman, Sly, and Hayward 1988) gen. nov., comb. nov., and Telluria chitinolytica sp. nov., soil-dwelling organisms which actively degrade polysaccharides. Int J Syst Bacteriol. 1993 Jan;43(1):120–124. doi: 10.1099/00207713-43-1-120. [DOI] [PubMed] [Google Scholar]
  14. Brenner D. J., Fanning G. R., Rake A. V., Johnson K. E. Batch procedure for thermal elution of DNA from hydroxyapatite. Anal Biochem. 1969 Apr 4;28(1):447–459. doi: 10.1016/0003-2697(69)90199-7. [DOI] [PubMed] [Google Scholar]
  15. Bronsdon M. A., Goodwin C. S., Sly L. I., Chilvers T., Schoenknecht F. D. Helicobacter nemestrinae sp. nov., a spiral bacterium found in the stomach of a pigtailed macaque (Macaca nemestrina) Int J Syst Bacteriol. 1991 Jan;41(1):148–153. doi: 10.1099/00207713-41-1-148. [DOI] [PubMed] [Google Scholar]
  16. Burnens A. P., Nicolet J. Three supplementary diagnostic tests for Campylobacter species and related organisms. J Clin Microbiol. 1993 Mar;31(3):708–710. doi: 10.1128/jcm.31.3.708-710.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Busse H. J., el-Banna T., Oyaizu H., Auling G. Identification of xenobiotic-degrading isolates from the beta subclass of the Proteobacteria by a polyphasic approach including 16S rRNA partial sequencing. Int J Syst Bacteriol. 1992 Jan;42(1):19–26. doi: 10.1099/00207713-42-1-19. [DOI] [PubMed] [Google Scholar]
  18. Caetano-Anollés G., Bassam B. J., Gresshoff P. M. DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Biotechnology (N Y) 1991 Jun;9(6):553–557. doi: 10.1038/nbt0691-553. [DOI] [PubMed] [Google Scholar]
  19. Camp R. C. Benchmarking--a conversation with Robert C. Camp. The source. Interview by Joe Flower. Healthc Forum J. 1993 Jan-Feb;36(1):30–36. [PubMed] [Google Scholar]
  20. Chevrier D., Larzul D., Megraud F., Guesdon J. L. Identification and classification of Campylobacter strains by using nonradioactive DNA probes. J Clin Microbiol. 1989 Feb;27(2):321–326. doi: 10.1128/jcm.27.2.321-326.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Clayton R. A., Sutton G., Hinkle P. S., Jr, Bult C., Fields C. Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int J Syst Bacteriol. 1995 Jul;45(3):595–599. doi: 10.1099/00207713-45-3-595. [DOI] [PubMed] [Google Scholar]
  22. Collins M. D., Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev. 1981 Jun;45(2):316–354. doi: 10.1128/mr.45.2.316-354.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Collins M. D., Samelis J., Metaxopoulos J., Wallbanks S. Taxonomic studies on some leuconostoc-like organisms from fermented sausages: description of a new genus Weissella for the Leuconostoc paramesenteroides group of species. J Appl Bacteriol. 1993 Dec;75(6):595–603. doi: 10.1111/j.1365-2672.1993.tb01600.x. [DOI] [PubMed] [Google Scholar]
  24. Collins M. D., Wallbanks S. Comparative sequence analyses of the 16S rRNA genes of Lactobacillus minutus, Lactobacillus rimae and Streptococcus parvulus: proposal for the creation of a new genus Atopobium. FEMS Microbiol Lett. 1992 Aug 15;74(2-3):235–240. doi: 10.1016/0378-1097(92)90435-q. [DOI] [PubMed] [Google Scholar]
  25. Coloe P. J., Slattery J. F., Cavanaugh P., Vaughan J. The cellular fatty acid composition of Campylobacter species isolated from cases of enteritis in man and animals. J Hyg (Lond) 1986 Apr;96(2):225–229. doi: 10.1017/s0022172400065992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Colwell R. R. Polyphasic taxonomy of the genus vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacteriol. 1970 Oct;104(1):410–433. doi: 10.1128/jb.104.1.410-433.1970. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Cookson B. T., Vandamme P., Carlson L. C., Larson A. M., Sheffield J. V., Kersters K., Spach D. H. Bacteremia caused by a novel Bordetella species, "B. hinzii". J Clin Microbiol. 1994 Oct;32(10):2569–2571. doi: 10.1128/jcm.32.10.2569-2571.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Costas M., Pot B., Vandamme P., Kersters K., Owen R. J., Hill L. R. Interlaboratory comparative study of the numerical analysis of one-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoretic protein patterns of Campylobacter strains. Electrophoresis. 1990 Jun;11(6):467–474. doi: 10.1002/elps.1150110606. [DOI] [PubMed] [Google Scholar]
  29. Crosa J. H., Brenner D. J., Falkow S. Use of a single-strand specific nuclease for analysis of bacterial and plasmid deoxyribonucleic acid homo- and heteroduplexes. J Bacteriol. 1973 Sep;115(3):904–911. doi: 10.1128/jb.115.3.904-911.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Curtis M. A. Cellular fatty acid profiles of campylobacters. Med Lab Sci. 1983 Oct;40(4):333–348. [PubMed] [Google Scholar]
  31. DAVIS G. H. The classification of Lactobacilli from the human mouth. J Gen Microbiol. 1955 Dec;13(3):481–493. doi: 10.1099/00221287-13-3-481. [DOI] [PubMed] [Google Scholar]
  32. De Ley J., Cattoir H., Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem. 1970 Jan;12(1):133–142. doi: 10.1111/j.1432-1033.1970.tb00830.x. [DOI] [PubMed] [Google Scholar]
  33. De Ley J., De Smedt J. Improvements of the membrane filter method for DNA:rRNA hybridization. Antonie Van Leeuwenhoek. 1975;41(3):287–307. doi: 10.1007/BF02565064. [DOI] [PubMed] [Google Scholar]
  34. De Ley J., Mannheim W., Mutters R., Piechulla K., Tytgat R., Segers P., Bisgaard M., Frederiksen W., Hinz K. H., Vanhoucke M. Inter- and intrafamilial similarities of rRNA cistrons of the Pasteurellaceae. Int J Syst Bacteriol. 1990 Apr;40(2):126–137. doi: 10.1099/00207713-40-2-126. [DOI] [PubMed] [Google Scholar]
  35. De Rijk P., Neefs J. M., Van de Peer Y., De Wachter R. Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 1992 May 11;20 (Suppl):2075–2089. doi: 10.1093/nar/20.suppl.2075. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Dellaglio F., Bottazzi V., Trovatelli L. D. Deoxyribonucleic acid homology and base composition in some thermophilic lactobacilli. J Gen Microbiol. 1973 Feb;74(2):289–297. doi: 10.1099/00221287-74-2-289. [DOI] [PubMed] [Google Scholar]
  37. Dennis P. J., Brenner D. J., Thacker W. L., Wait R., Vesey G., Steigerwalt A. G., Benson R. F. Five new Legionella species isolated from water. Int J Syst Bacteriol. 1993 Apr;43(2):329–337. doi: 10.1099/00207713-43-2-329. [DOI] [PubMed] [Google Scholar]
  38. Devriese L. A., Pot B., Van Damme L., Kersters K., Haesebrouck F. Identification of Enterococcus species isolated from foods of animal origin. Int J Food Microbiol. 1995 Jul;26(2):187–197. doi: 10.1016/0168-1605(94)00119-q. [DOI] [PubMed] [Google Scholar]
  39. Dewhirst F. E., Chen C. K., Paster B. J., Zambon J. J. Phylogeny of species in the family Neisseriaceae isolated from human dental plaque and description of Kingella oralis sp. nov [corrected]. Int J Syst Bacteriol. 1993 Jul;43(3):490–499. doi: 10.1099/00207713-43-3-490. [DOI] [PubMed] [Google Scholar]
  40. Dewhirst F. E., Paster B. J., La Fontaine S., Rood J. I. Transfer of Kingella indologenes (Snell and Lapage 1976) to the genus Suttonella gen. nov. as Suttonella indologenes comb. nov.; transfer of Bacteroides nodosus (Beveridge 1941) to the genus Dichelobacter gen. nov. as Dichelobacter nodosus comb. nov.; and assignment of the genera Cardiobacterium, Dichelobacter, and Suttonella to Cardiobacteriaceae fam. nov. in the gamma division of Proteobacteria on the basis of 16S rRNA sequence comparisons. Int J Syst Bacteriol. 1990 Oct;40(4):426–433. doi: 10.1099/00207713-40-4-426. [DOI] [PubMed] [Google Scholar]
  41. Dewhirst F. E., Paster B. J., Olsen I., Fraser G. J. Phylogeny of 54 representative strains of species in the family Pasteurellaceae as determined by comparison of 16S rRNA sequences. J Bacteriol. 1992 Mar;174(6):2002–2013. doi: 10.1128/jb.174.6.2002-2013.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Dewhirst F. E., Seymour C., Fraser G. J., Paster B. J., Fox J. G. Phylogeny of Helicobacter isolates from bird and swine feces and description of Helicobacter pametensis sp. nov. Int J Syst Bacteriol. 1994 Jul;44(3):553–560. doi: 10.1099/00207713-44-3-553. [DOI] [PubMed] [Google Scholar]
  43. Dicks L. M., Dellaglio F., Collins M. D. Proposal to reclassify Leuconostoc oenos as Oenococcus oeni [corrig.] gen. nov., comb. nov.. Int J Syst Bacteriol. 1995 Apr;45(2):395–397. doi: 10.1099/00207713-45-2-395. [DOI] [PubMed] [Google Scholar]
  44. Du Y., McLaughlin G., Chang K. P. 16S ribosomal DNA sequence identities of beta-proteobacterial endosymbionts in three Crithidia species. J Bacteriol. 1994 May;176(10):3081–3084. doi: 10.1128/jb.176.10.3081-3084.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. EFTHYMIOU C., HANSEN P. A. An antigenic analysis of Lactobacillus acidophilus. J Infect Dis. 1962 May-Jun;110:258–267. doi: 10.1093/infdis/110.3.258. [DOI] [PubMed] [Google Scholar]
  46. Eaton K. A., Dewhirst F. E., Radin M. J., Fox J. G., Paster B. J., Krakowka S., Morgan D. R. Helicobacter acinonyx sp. nov., isolated from cheetahs with gastritis. Int J Syst Bacteriol. 1993 Jan;43(1):99–106. doi: 10.1099/00207713-43-1-99. [DOI] [PubMed] [Google Scholar]
  47. Elliott J. A., Collins M. D., Pigott N. E., Facklam R. R. Differentiation of Lactococcus lactis and Lactococcus garvieae from humans by comparison of whole-cell protein patterns. J Clin Microbiol. 1991 Dec;29(12):2731–2734. doi: 10.1128/jcm.29.12.2731-2734.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Etoh Y., Dewhirst F. E., Paster B. J., Yamamoto A., Goto N. Campylobacter showae sp. nov., isolated from the human oral cavity. Int J Syst Bacteriol. 1993 Oct;43(4):631–639. doi: 10.1099/00207713-43-4-631. [DOI] [PubMed] [Google Scholar]
  49. Eyers M., Chapelle S., Van Camp G., Goossens H., De Wachter R. Discrimination among thermophilic Campylobacter species by polymerase chain reaction amplification of 23S rRNA gene fragments. J Clin Microbiol. 1994 Jun;32(6):1623–1623. doi: 10.1128/jcm.32.6.1623-.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Ferguson D. A., Jr, Lambe D. W., Jr Differentiation of Campylobacter species by protein banding patterns in polyacrylamide slab gels. J Clin Microbiol. 1984 Sep;20(3):453–460. doi: 10.1128/jcm.20.3.453-460.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Fischer W., Koch H. U., Haas R. Improved preparation of lipoteichoic acids. Eur J Biochem. 1983 Jul 1;133(3):523–530. doi: 10.1111/j.1432-1033.1983.tb07495.x. [DOI] [PubMed] [Google Scholar]
  52. Fischer W., Koch H. U., Rösel P., Fiedler F. Alanine ester-containing native lipoteichoic acids do not act as lipoteichoic acid carrier. Isolation, structural and functional characterization. J Biol Chem. 1980 May 25;255(10):4557–4562. [PubMed] [Google Scholar]
  53. Fischer W., Rösel P., Koch H. U. Effect of alanine ester substitution and other structural features of lipoteichoic acids on their inhibitory activity against autolysins of Staphylococcus aureus. J Bacteriol. 1981 May;146(2):467–475. doi: 10.1128/jb.146.2.467-475.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Flores B. M., Fennell C. L., Stamm W. E. Characterization of Campylobacter cinaedi and C. fennelliae antigens and analysis of the human immune response. J Infect Dis. 1989 Apr;159(4):635–640. doi: 10.1093/infdis/159.4.635. [DOI] [PubMed] [Google Scholar]
  55. Fox G. E., Wisotzkey J. D., Jurtshuk P., Jr How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol. 1992 Jan;42(1):166–170. doi: 10.1099/00207713-42-1-166. [DOI] [PubMed] [Google Scholar]
  56. Fox J. G., Dewhirst F. E., Tully J. G., Paster B. J., Yan L., Taylor N. S., Collins M. J., Jr, Gorelick P. L., Ward J. M. Helicobacter hepaticus sp. nov., a microaerophilic bacterium isolated from livers and intestinal mucosal scrapings from mice. J Clin Microbiol. 1994 May;32(5):1238–1245. doi: 10.1128/jcm.32.5.1238-1245.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Fox J. G., Yan L. L., Dewhirst F. E., Paster B. J., Shames B., Murphy J. C., Hayward A., Belcher J. C., Mendes E. N. Helicobacter bilis sp. nov., a novel Helicobacter species isolated from bile, livers, and intestines of aged, inbred mice. J Clin Microbiol. 1995 Feb;33(2):445–454. doi: 10.1128/jcm.33.2.445-454.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Fujisawa T., Benno Y., Yaeshima T., Mitsuoka T. Taxonomic study of the Lactobacillus acidophilus group, with recognition of Lactobacillus gallinarum sp. nov. and Lactobacillus johnsonii sp. nov. and synonymy of Lactobacillus acidophilus group A3 (Johnson et al. 1980) with the type strain of Lactobacillus amylovorus (Nakamura 1981). Int J Syst Bacteriol. 1992 Jul;42(3):487–491. doi: 10.1099/00207713-42-3-487. [DOI] [PubMed] [Google Scholar]
  59. Gasser F. Electrophoretic characterization of lactic dehydrogenases in the genus Lactobacillus. J Gen Microbiol. 1970 Aug;62(2):223–239. doi: 10.1099/00221287-62-2-223. [DOI] [PubMed] [Google Scholar]
  60. Gasser F., Gasser C. Immunological relationships among lactic dehydrogenases in the genera Lactobacillus and Leuconostoc. J Bacteriol. 1971 Apr;106(1):113–125. doi: 10.1128/jb.106.1.113-125.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Gilliland S. E. Acidophilus milk products: a review of potential benefits to consumers. J Dairy Sci. 1989 Oct;72(10):2483–2494. doi: 10.3168/jds.S0022-0302(89)79389-9. [DOI] [PubMed] [Google Scholar]
  62. Goodwin C. S., McConnell W., McCulloch R. K., McCullough C., Hill R., Bronsdon M. A., Kasper G. Cellular fatty acid composition of Campylobacter pylori from primates and ferrets compared with those of other campylobacters. J Clin Microbiol. 1989 May;27(5):938–943. doi: 10.1128/jcm.27.5.938-943.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  63. Goossens H., Giesendorf B. A., Vandamme P., Vlaes L., Van den Borre C., Koeken A., Quint W. G., Blomme W., Hanicq P., Koster D. S. Investigation of an outbreak of Campylobacter upsaliensis in day care centers in Brussels: analysis of relationships among isolates by phenotypic and genotypic typing methods. J Infect Dis. 1995 Nov;172(5):1298–1305. doi: 10.1093/infdis/172.5.1298. [DOI] [PubMed] [Google Scholar]
  64. Goossens H., Pot B., Vlaes L., Van den Borre C., Van den Abbeele R., Van Naelten C., Levy J., Cogniau H., Marbehant P., Verhoef J. Characterization and description of "Campylobacter upsaliensis" isolated from human feces. J Clin Microbiol. 1990 May;28(5):1039–1046. doi: 10.1128/jcm.28.5.1039-1046.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. Gordillo M. E., Singh K. V., Baker C. J., Murray B. E. Typing of group B streptococci: comparison of pulsed-field gel electrophoresis and conventional electrophoresis. J Clin Microbiol. 1993 Jun;31(6):1430–1434. doi: 10.1128/jcm.31.6.1430-1434.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Grimont F., Grimont P. A. Ribosomal ribonucleic acid gene restriction patterns as potential taxonomic tools. Ann Inst Pasteur Microbiol. 1986 Sep-Oct;137B(2):165–175. doi: 10.1016/s0769-2609(86)80105-3. [DOI] [PubMed] [Google Scholar]
  67. Grimont P. A. Use of DNA reassociation in bacterial classification. Can J Microbiol. 1988 Apr;34(4):541–546. doi: 10.1139/m88-092. [DOI] [PubMed] [Google Scholar]
  68. Gurtler V., Wilson V. A., Mayall B. C. Classification of medically important clostridia using restriction endonuclease site differences of PCR-amplified 16S rDNA. J Gen Microbiol. 1991 Nov;137(11):2673–2679. doi: 10.1099/00221287-137-11-2673. [DOI] [PubMed] [Google Scholar]
  69. Gutell R. R., Larsen N., Woese C. R. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev. 1994 Mar;58(1):10–26. doi: 10.1128/mr.58.1.10-26.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  70. Han Y. H., Smibert R. M., Krieg N. R. Cytochrome composition and oxygen-dependent respiration-driven proton translocation in Wolinella curva, Wolinella recta, Bacteroides ureolyticus, and Bacteroides gracilis. Can J Microbiol. 1992 Feb;38(2):104–110. doi: 10.1139/m92-017. [DOI] [PubMed] [Google Scholar]
  71. Han Y. H., Smibert R. M., Krieg N. R. Wolinella recta, Wolinella curva, Bacteroides ureolyticus, and Bacteroides gracilis are microaerophiles, not anaerobes. Int J Syst Bacteriol. 1991 Apr;41(2):218–222. doi: 10.1099/00207713-41-2-218. [DOI] [PubMed] [Google Scholar]
  72. Hensel R., Mayr U., Stetter K. O., Kandler O. Comparative studies of lactic acid dehydrogenases in lactic acid bacteria. I. Purification and kinetics of the allosteric L-lactic acid dehydrogenase from Lactobacillus casei ssp. casei and Lactobacillus curvatus. Arch Microbiol. 1977 Feb 4;112(1):81–93. doi: 10.1007/BF00446658. [DOI] [PubMed] [Google Scholar]
  73. Hodge D. S., Borczyk A., Wat L. L. Evaluation of the indoxyl acetate hydrolysis test for the differentiation of Campylobacters. J Clin Microbiol. 1990 Jun;28(6):1482–1483. doi: 10.1128/jcm.28.6.1482-1483.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  74. Hébert G. A., Edmonds P., Brenner D. J. DNA relatedness among strains of Campylobacter jejuni and Campylobacter coli with divergent serogroup and hippurate reactions. J Clin Microbiol. 1984 Jul;20(1):138–140. doi: 10.1128/jcm.20.1.138-140.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  75. Hébert G. A., Hollis D. G., Weaver R. E., Lambert M. A., Blaser M. J., Moss C. W. 30 years of campylobacters: biochemical characteristics and a biotyping proposal for Campylobacter jejuni. J Clin Microbiol. 1982 Jun;15(6):1065–1073. doi: 10.1128/jcm.15.6.1065-1073.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  76. Jarvis A. W., Wolff J. M. Grouping of lactic streptococci by gel electrophoresis of soluble cell extracts. Appl Environ Microbiol. 1979 Mar;37(3):391–398. doi: 10.1128/aem.37.3.391-398.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  77. Jayarao B. M., Doré J. J., Jr, Baumbach G. A., Matthews K. R., Oliver S. P. Differentiation of Streptococcus uberis from Streptococcus parauberis by polymerase chain reaction and restriction fragment length polymorphism analysis of 16S ribosomal DNA. J Clin Microbiol. 1991 Dec;29(12):2774–2778. doi: 10.1128/jcm.29.12.2774-2778.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  78. Jenkins C. L., Starr M. P. Formation of halogenated aryl-polyene (xanthomonadin) pigments by the type and other yellow-pigmented strains of Xanthomonas maltophilia. Ann Inst Pasteur Microbiol. 1985 Nov-Dec;136B(3):257–264. doi: 10.1016/s0769-2609(85)80071-5. [DOI] [PubMed] [Google Scholar]
  79. Kersters K., De Ley J. Identification and grouping of bacteria by numerical analysis of their electrophoretic protein patterns. J Gen Microbiol. 1975 Apr;87(2):333–342. doi: 10.1099/00221287-87-2-333. [DOI] [PubMed] [Google Scholar]
  80. Klijn N., Weerkamp A. H., de Vos W. M. Identification of mesophilic lactic acid bacteria by using polymerase chain reaction-amplified variable regions of 16S rRNA and specific DNA probes. Appl Environ Microbiol. 1991 Nov;57(11):3390–3393. doi: 10.1128/aem.57.11.3390-3393.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  81. Knox K. W., Wicken A. J. Immunological properties of teichoic acids. Bacteriol Rev. 1973 Jun;37(2):215–257. doi: 10.1128/br.37.2.215-257.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  82. Kostman J. R., Edlind T. D., LiPuma J. J., Stull T. L. Molecular epidemiology of Pseudomonas cepacia determined by polymerase chain reaction ribotyping. J Clin Microbiol. 1992 Aug;30(8):2084–2087. doi: 10.1128/jcm.30.8.2084-2087.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  83. Laguerre G., Allard M. R., Revoy F., Amarger N. Rapid Identification of Rhizobia by Restriction Fragment Length Polymorphism Analysis of PCR-Amplified 16S rRNA Genes. Appl Environ Microbiol. 1994 Jan;60(1):56–63. doi: 10.1128/aem.60.1.56-63.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  84. Lambert M. A., Patton C. M., Barrett T. J., Moss C. W. Differentiation of Campylobacter and Campylobacter-like organisms by cellular fatty acid composition. J Clin Microbiol. 1987 Apr;25(4):706–713. doi: 10.1128/jcm.25.4.706-713.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  85. Lane D. J., Pace B., Olsen G. J., Stahl D. A., Sogin M. L., Pace N. R. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985 Oct;82(20):6955–6959. doi: 10.1073/pnas.82.20.6955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  86. Lau P. P., DeBrunner-Vossbrinck B., Dunn B., Miotto K., MacDonnell M. T., Rollins D. M., Pillidge C. J., Hespell R. B., Colwell R. R., Sogin M. L. Phylogenetic diversity and position of the genus Campylobacter. Syst Appl Microbiol. 1987;9:231–238. doi: 10.1016/s0723-2020(87)80027-9. [DOI] [PubMed] [Google Scholar]
  87. Le Bras G., Garel J. R. Properties of D-lactate dehydrogenase from Lactobacillus bulgaricus: a possible different evolutionary origin for the D- and L-lactate dehydrogenases. FEMS Microbiol Lett. 1991 Mar 15;63(1):89–93. doi: 10.1016/0378-1097(91)90533-g. [DOI] [PubMed] [Google Scholar]
  88. Lee A., Phillips M. W., O'Rourke J. L., Paster B. J., Dewhirst F. E., Fraser G. J., Fox J. G., Sly L. I., Romaniuk P. J., Trust T. J. Helicobacter muridarum sp. nov., a microaerophilic helical bacterium with a novel ultrastructure isolated from the intestinal mucosa of rodents. Int J Syst Bacteriol. 1992 Jan;42(1):27–36. doi: 10.1099/00207713-42-1-27. [DOI] [PubMed] [Google Scholar]
  89. London J., Chace N. M. Aldolases of the lactic acid bacteria. Demonstration of immunological relationships among eight genera of Gram positive bacteria using an anti-pediococcal aldolase serum. Arch Microbiol. 1976 Oct 11;110(1):121–128. doi: 10.1007/BF00416976. [DOI] [PubMed] [Google Scholar]
  90. London J., Kline K. Aldolase of lactic acid bacteria: a case history in the use of an enzyme as an evolutionary marker. Bacteriol Rev. 1973 Dec;37(4):453–478. doi: 10.1128/br.37.4.453-478.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  91. London J., Meyer E. Y., Kulczyk S. R. Detection of relationships between Streptococcus faecalis and Lactobacillus casei by immunological studies with two forms of malic enzyme. J Bacteriol. 1971 Oct;108(1):196–201. doi: 10.1128/jb.108.1.196-201.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  92. London J., Meyer E. Y., Kulczyk S. Comparative biochemical and immunological study of malic enzyme from two species of lactic acid bacteria: evolutionary implications. J Bacteriol. 1971 Apr;106(1):126–137. doi: 10.1128/jb.106.1.126-137.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  93. Ludwig W., Neumaier J., Klugbauer N., Brockmann E., Roller C., Jilg S., Reetz K., Schachtner I., Ludvigsen A., Bachleitner M. Phylogenetic relationships of Bacteria based on comparative sequence analysis of elongation factor Tu and ATP-synthase beta-subunit genes. Antonie Van Leeuwenhoek. 1993;64(3-4):285–305. doi: 10.1007/BF00873088. [DOI] [PubMed] [Google Scholar]
  94. Lupski J. R., Weinstock G. M. Short, interspersed repetitive DNA sequences in prokaryotic genomes. J Bacteriol. 1992 Jul;174(14):4525–4529. doi: 10.1128/jb.174.14.4525-4529.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  95. MARMUR J., DOTY P. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol. 1962 Jul;5:109–118. doi: 10.1016/s0022-2836(62)80066-7. [DOI] [PubMed] [Google Scholar]
  96. Macy J. M., Rech S., Auling G., Dorsch M., Stackebrandt E., Sly L. I. Thauera selenatis gen. nov., sp. nov., a member of the beta subclass of Proteobacteria with a novel type of anaerobic respiration. Int J Syst Bacteriol. 1993 Jan;43(1):135–142. doi: 10.1099/00207713-43-1-135. [DOI] [PubMed] [Google Scholar]
  97. Martinez-Murcia A. J., Collins M. D. A phylogenetic analysis of an atypical leuconostoc: description of Leuconostoc fallax sp. nov. FEMS Microbiol Lett. 1991 Jul 15;66(1):55–59. doi: 10.1016/0378-1097(91)90420-f. [DOI] [PubMed] [Google Scholar]
  98. Maslow J. N., Mulligan M. E., Arbeit R. D. Molecular epidemiology: application of contemporary techniques to the typing of microorganisms. Clin Infect Dis. 1993 Aug;17(2):153–164. doi: 10.1093/clinids/17.2.153. [DOI] [PubMed] [Google Scholar]
  99. McClelland M., Petersen C., Welsh J. Length polymorphisms in tRNA intergenic spacers detected by using the polymerase chain reaction can distinguish streptococcal strains and species. J Clin Microbiol. 1992 Jun;30(6):1499–1504. doi: 10.1128/jcm.30.6.1499-1504.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  100. McNulty C. A., Dent J. C., Curry A., Uff J. S., Ford G. A., Gear M. W., Wilkinson S. P. New spiral bacterium in gastric mucosa. J Clin Pathol. 1989 Jun;42(6):585–591. doi: 10.1136/jcp.42.6.585. [DOI] [PMC free article] [PubMed] [Google Scholar]
  101. Megraud F., Bonnet F., Garnier M., Lamouliatte H. Characterization of "Campylobacter pyloridis" by culture, enzymatic profile, and protein content. J Clin Microbiol. 1985 Dec;22(6):1007–1010. doi: 10.1128/jcm.22.6.1007-1010.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  102. Mendes E. N., Queiroz D. M., Rocha G. A., Moura S. B., Leite V. H., Fonseca M. E. Ultrastructure of a spiral micro-organism from pig gastric mucosa ("Gastrospirillum suis"). J Med Microbiol. 1990 Sep;33(1):61–66. doi: 10.1099/00222615-33-1-61. [DOI] [PubMed] [Google Scholar]
  103. Mills C. K., Gherna R. L. Hydrolysis of indoxyl acetate by Campylobacter species. J Clin Microbiol. 1987 Aug;25(8):1560–1561. doi: 10.1128/jcm.25.8.1560-1561.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  104. Mitsuoka T. Vergleichende Untersuchungen über die Laktobazillen aus den Faeces von Menschen, Schweinen und Hühnern. Zentralbl Bakteriol Orig. 1969 May;210(1):32–51. [PubMed] [Google Scholar]
  105. Morotomi M., Hoshina S., Green P., Neu H. C., LoGerfo P., Watanabe I., Mutai M., Weinstein I. B. Oligonucleotide probe for detection and identification of Campylobacter pylori. J Clin Microbiol. 1989 Dec;27(12):2652–2655. doi: 10.1128/jcm.27.12.2652-2655.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  106. Morris J. A., Park R. W. A comparison using gel electrophoresis of cell proteins of campylobacters (vibrios) associated with infertility, abortion and swine dysentery. J Gen Microbiol. 1973 Sep;78(1):165–178. doi: 10.1099/00221287-78-1-165. [DOI] [PubMed] [Google Scholar]
  107. Moss C. W., Kai A., Lambert M. A., Patton C. Isoprenoid quinone content and cellular fatty acid composition of Campylobacter species. J Clin Microbiol. 1984 Jun;19(6):772–776. doi: 10.1128/jcm.19.6.772-776.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  108. Moss C. W., Lambert-Fair M. A., Nicholson M. A., Guerrant G. O. Isoprenoid quinones of Campylobacter cryaerophila, C. cinaedi, C. fennelliae, C. hyointestinalis, C. pylori, and "C. upsaliensis". J Clin Microbiol. 1990 Feb;28(2):395–397. doi: 10.1128/jcm.28.2.395-397.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  109. Murray R. G., Schleifer K. H. Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes. Int J Syst Bacteriol. 1994 Jan;44(1):174–176. doi: 10.1099/00207713-44-1-174. [DOI] [PubMed] [Google Scholar]
  110. Naas T., Blot M., Fitch W. M., Arber W. Dynamics of IS-related genetic rearrangements in resting Escherichia coli K-12. Mol Biol Evol. 1995 Mar;12(2):198–207. doi: 10.1093/oxfordjournals.molbev.a040198. [DOI] [PubMed] [Google Scholar]
  111. Nour S. M., Fernandez M. P., Normand P., Cleyet-Marel J. C. Rhizobium ciceri sp. nov., consisting of strains that nodulate chickpeas (Cicer arietinum L.). Int J Syst Bacteriol. 1994 Jul;44(3):511–522. doi: 10.1099/00207713-44-3-511. [DOI] [PubMed] [Google Scholar]
  112. Ochi K. Comparative ribosomal protein sequence analyses of a phylogenetically defined genus, Pseudomonas, and its relatives. Int J Syst Bacteriol. 1995 Apr;45(2):268–273. doi: 10.1099/00207713-45-2-268. [DOI] [PubMed] [Google Scholar]
  113. Ohya T., Kubo M., Watase H. Electrophoretic protein patterns in Campylobacter species with special reference to Campylobacter mucosalis and Campylobacter hyointestinalis. Nihon Juigaku Zasshi. 1988 Jun;50(3):692–698. doi: 10.1292/jvms1939.50.692. [DOI] [PubMed] [Google Scholar]
  114. Olsen G. J., Larsen N., Woese C. R. The ribosomal RNA database project. Nucleic Acids Res. 1991 Apr 25;19 (Suppl):2017–2021. doi: 10.1093/nar/19.suppl.2017. [DOI] [PMC free article] [PubMed] [Google Scholar]
  115. On S. L., Holmes B. Assessment of enzyme detection tests useful in identification of campylobacteria. J Clin Microbiol. 1992 Mar;30(3):746–749. doi: 10.1128/jcm.30.3.746-749.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  116. On S. L., Holmes B. Reproducibility of tolerance tests that are useful in the identification of campylobacteria. J Clin Microbiol. 1991 Sep;29(9):1785–1788. doi: 10.1128/jcm.29.9.1785-1788.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  117. Owen R. J., Costas M., Morgan D. D., On S. L., Hill L. R., Pearson A. D., Morgan D. R. Strain variation in Campylobacter pylori detected by numerical analysis of one-dimensional electrophoretic protein patterns. Antonie Van Leeuwenhoek. 1989 Mar;55(3):253–267. doi: 10.1007/BF00393854. [DOI] [PubMed] [Google Scholar]
  118. Owen R. J., Costas M., Sloss L. L. Electrophoretic protein typing of Campylobacter jejuni subspecies "doylei" (nitrate-negative campylobacter-like organisms) from human faeces and gastric mucosa. Eur J Epidemiol. 1988 Sep;4(3):277–283. doi: 10.1007/BF00148910. [DOI] [PubMed] [Google Scholar]
  119. Owen R. J., Costas M., Sloss L., Bolton F. J. Numerical analysis of electrophoretic protein patterns of Campylobacter laridis and allied thermophilic campylobacters from the natural environment. J Appl Bacteriol. 1988 Jul;65(1):69–78. doi: 10.1111/j.1365-2672.1988.tb04319.x. [DOI] [PubMed] [Google Scholar]
  120. Owen R. J., Jackman P. J. The similarities between Pseudomonas paucimobilis and allied bacteria derived from analysis of deoxyribonucleic acids and electrophoretic protein patterns. J Gen Microbiol. 1982 Dec;128(12):2945–2954. doi: 10.1099/00221287-128-12-2945. [DOI] [PubMed] [Google Scholar]
  121. Owen R. J., Morgan D. D., Costas M., Lastovica A. Identification of 'Campylobacter upsaliensis' and other catalase-negative campylobacters from paediatric blood cultures by numerical analysis of electrophoretic protein patterns. FEMS Microbiol Lett. 1989 Apr;49(2-3):145–150. doi: 10.1016/0378-1097(89)90029-3. [DOI] [PubMed] [Google Scholar]
  122. Palleroni N. J., Bradbury J. F. Stenotrophomonas, a new bacterial genus for Xanthomonas maltophilia (Hugh 1980) Swings et al. 1983. Int J Syst Bacteriol. 1993 Jul;43(3):606–609. doi: 10.1099/00207713-43-3-606. [DOI] [PubMed] [Google Scholar]
  123. Paster B. J., Lee A., Fox J. G., Dewhirst F. E., Tordoff L. A., Fraser G. J., O'Rourke J. L., Taylor N. S., Ferrero R. Phylogeny of Helicobacter felis sp. nov., Helicobacter mustelae, and related bacteria. Int J Syst Bacteriol. 1991 Jan;41(1):31–38. doi: 10.1099/00207713-41-1-31. [DOI] [PubMed] [Google Scholar]
  124. Pearson A. D., Ireland A., Bamforth J., Walker C., Booth L., Hawtin P., Holdstock G., Millward-Sadler H. Polyacrylamide gel electrophoresis of spiral bacteria from the gastric antrum. Lancet. 1984 Jun 16;1(8390):1349–1350. doi: 10.1016/s0140-6736(84)91837-3. [DOI] [PubMed] [Google Scholar]
  125. Pheasant H., Bursk A., Goldfarb J., Azen S. P., Weiss J. N., Borelli L. Amitriptyline and chronic low-back pain. A randomized double-blind crossover study. Spine (Phila Pa 1976) 1983 Jul-Aug;8(5):552–557. doi: 10.1097/00007632-198307000-00012. [DOI] [PubMed] [Google Scholar]
  126. Popoff M., Coynault C. Use of DEAE-cellulose filters in the S1 nuclease method for bacterial deoxyribonucleic acid hybridization. Ann Microbiol (Paris) 1980 Mar-Apr;131A(2):151–155. [PubMed] [Google Scholar]
  127. Popovic-Uroic T., Patton C. M., Nicholson M. A., Kiehlbauch J. A. Evaluation of the indoxyl acetate hydrolysis test for rapid differentiation of Campylobacter, Helicobacter, and Wolinella species. J Clin Microbiol. 1990 Oct;28(10):2335–2339. doi: 10.1128/jcm.28.10.2335-2339.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  128. Pot B., Devriese L. A., Hommez J., Miry C., Vandemeulebroecke K., Kersters K., Haesebrouck F. Characterization and identification of Vagococcus fluvialis strains isolated from domestic animals. J Appl Bacteriol. 1994 Oct;77(4):362–369. doi: 10.1111/j.1365-2672.1994.tb03436.x. [DOI] [PubMed] [Google Scholar]
  129. Pot B., Hertel C., Ludwig W., Descheemaeker P., Kersters K., Schleifer K. H. Identification and classification of Lactobacillus acidophilus, L. gasseri and L. johnsonii strains by SDS-PAGE and rRNA-targeted oligonucleotide probe hybridization. J Gen Microbiol. 1993 Mar;139(3):513–517. doi: 10.1099/00221287-139-3-513. [DOI] [PubMed] [Google Scholar]
  130. Ralph D., McClelland M., Welsh J., Baranton G., Perolat P. Leptospira species categorized by arbitrarily primed polymerase chain reaction (PCR) and by mapped restriction polymorphisms in PCR-amplified rRNA genes. J Bacteriol. 1993 Feb;175(4):973–981. doi: 10.1128/jb.175.4.973-981.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  131. Reuter G. Zusammensetzung und Anwendung von Bakterienkulturen für therapeutische Zwecke. Arzneimittelforschung. 1969 Jan;19(1):103–109. [PubMed] [Google Scholar]
  132. Romaniuk P. J., Zoltowska B., Trust T. J., Lane D. J., Olsen G. J., Pace N. R., Stahl D. A. Campylobacter pylori, the spiral bacterium associated with human gastritis, is not a true Campylobacter sp. J Bacteriol. 1987 May;169(5):2137–2141. doi: 10.1128/jb.169.5.2137-2141.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  133. Roop R. M., 2nd, Smibert R. M., Johnson J. L., Krieg N. R. DNA homology studies of the catalase-negative campylobacters and "Campylobacter fecalis," an emended description of Campylobacter sputorum, and proposal of the neotype strain of Campylobacter sputorum. Can J Microbiol. 1985 Sep;31(9):823–831. doi: 10.1139/m85-154. [DOI] [PubMed] [Google Scholar]
  134. Roop R. M., 2nd, Smibert R. M., Johnson J. L., Krieg N. R. Differential characteristics of catalase-positive campylobacters correlated with DNA homology groups. Can J Microbiol. 1984 Jul;30(7):938–951. doi: 10.1139/m84-147. [DOI] [PubMed] [Google Scholar]
  135. SEBALD M., VERON M. TENEUR EN BASES DE L'ADN ET CLASSIFICATION DES VIBRIONS. Ann Inst Pasteur (Paris) 1963 Nov;105:897–910. [PubMed] [Google Scholar]
  136. Salama M., Sandine W., Giovannoni S. Development and application of oligonucleotide probes for identification of Lactococcus lactis subsp. cremoris. Appl Environ Microbiol. 1991 May;57(5):1313–1318. doi: 10.1128/aem.57.5.1313-1318.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  137. Scherer P., Kneifel H. Distribution of polyamines in methanogenic bacteria. J Bacteriol. 1983 Jun;154(3):1315–1322. doi: 10.1128/jb.154.3.1315-1322.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  138. Schleifer K. H., Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev. 1972 Dec;36(4):407–477. doi: 10.1128/br.36.4.407-477.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  139. Seal S. E., Jackson L. A., Daniels M. J. Use of tRNA consensus primers to indicate subgroups of Pseudomonas solanacearum by polymerase chain reaction amplification. Appl Environ Microbiol. 1992 Nov;58(11):3759–3761. doi: 10.1128/aem.58.11.3759-3761.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  140. Segers P., Vancanneyt M., Pot B., Torck U., Hoste B., Dewettinck D., Falsen E., Kersters K., De Vos P. Classification of Pseudomonas diminuta Leifson and Hugh 1954 and Pseudomonas vesicularis Büsing, Döll, and Freytag 1953 in Brevundimonas gen. nov. as Brevundimonas diminuta comb. nov. and Brevundimonas vesicularis comb. nov., respectively. Int J Syst Bacteriol. 1994 Jul;44(3):499–510. doi: 10.1099/00207713-44-3-499. [DOI] [PubMed] [Google Scholar]
  141. Selander R. K., Caugant D. A., Ochman H., Musser J. M., Gilmour M. N., Whittam T. S. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl Environ Microbiol. 1986 May;51(5):873–884. doi: 10.1128/aem.51.5.873-884.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  142. Simonds J., Hansen P. A., Lakshmanan S. Deoxyribonucleic acid hybridization among strains of lactobacilli. J Bacteriol. 1971 Jul;107(1):382–384. doi: 10.1128/jb.107.1.382-384.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  143. Siverio F., Cambra M., Gorris M. T., Corzo J., Lopez M. M. Lipopolysaccharides as Determinants of Serological Variability in Pseudomonas corrugata. Appl Environ Microbiol. 1993 Jun;59(6):1805–1812. doi: 10.1128/aem.59.6.1805-1812.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  144. Solnick J. V., O'Rourke J., Lee A., Paster B. J., Dewhirst F. E., Tompkins L. S. An uncultured gastric spiral organism is a newly identified Helicobacter in humans. J Infect Dis. 1993 Aug;168(2):379–385. doi: 10.1093/infdis/168.2.379. [DOI] [PubMed] [Google Scholar]
  145. Stanley J., Burnens A. P., Linton D., On S. L., Costas M., Owen R. J. Campylobacter helveticus sp. nov., a new thermophilic species from domestic animals: characterization, and cloning of a species-specific DNA probe. J Gen Microbiol. 1992 Nov;138(11):2293–2303. doi: 10.1099/00221287-138-11-2293. [DOI] [PubMed] [Google Scholar]
  146. Stanley J., Linton D., Burnens A. P., Dewhirst F. E., Owen R. J., Porter A., On S. L., Costas M. Helicobacter canis sp. nov., a new species from dogs: an integrated study of phenotype and genotype. J Gen Microbiol. 1993 Oct;139(10):2495–2504. doi: 10.1099/00221287-139-10-2495. [DOI] [PubMed] [Google Scholar]
  147. Starr M. P., Jenkins C. L., Bussey L. B., Andrewes A. G. Chemotaxonomic significance of the xanthomonadins, novel brominated aryl-polyene pigments produced by bacteria of the genus Xanthomonas. Arch Microbiol. 1977 May 13;113(1-2):1–9. doi: 10.1007/BF00428572. [DOI] [PubMed] [Google Scholar]
  148. Subramaniam P., Bhatnagar R., Hooper A., Jensen R. A. The dynamic progression of evolved character states for aromatic amino acid biosynthesis in gram-negative bacteria. Microbiology. 1994 Dec;140(Pt 12):3431–3440. doi: 10.1099/13500872-140-12-3431. [DOI] [PubMed] [Google Scholar]
  149. Tabor C. W., Tabor H. Polyamines in microorganisms. Microbiol Rev. 1985 Mar;49(1):81–99. doi: 10.1128/mr.49.1.81-99.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  150. Tanner A. C. Characterization of Wolinella spp., Campylobacter concisus, Bacteroides gracilis, and Eikenella corrodens by polyacrylamide gel electrophoresis. J Clin Microbiol. 1986 Oct;24(4):562–565. doi: 10.1128/jcm.24.4.562-565.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  151. Tenover F. C., Arbeit R. D., Goering R. V., Mickelsen P. A., Murray B. E., Persing D. H., Swaminathan B. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol. 1995 Sep;33(9):2233–2239. doi: 10.1128/jcm.33.9.2233-2239.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  152. Ullman J. S., McCarthy B. J. The relationship between mismatched base pairs and the thermal stability of DNA duplexes. II. Effects of deamination of cytosine. Biochim Biophys Acta. 1973 Feb 4;294(1):416–424. doi: 10.1016/0005-2787(73)90096-8. [DOI] [PubMed] [Google Scholar]
  153. Ursing J., Sandstedt K., Hansson E. Genetic and phenotypic characteristics of a new group of Campylobacter isolated from pigs and cattle. Acta Pathol Microbiol Immunol Scand B. 1984 Feb;92(1):71–72. doi: 10.1111/j.1699-0463.1984.tb02796.x. [DOI] [PubMed] [Google Scholar]
  154. Van den Mooter M., Swings J. Numerical analysis of 295 phenotypic features of 266 Xanthomonas strains and related strains and an improved taxonomy of the genus. Int J Syst Bacteriol. 1990 Oct;40(4):348–369. doi: 10.1099/00207713-40-4-348. [DOI] [PubMed] [Google Scholar]
  155. Vandamme P., Daneshvar M. I., Dewhirst F. E., Paster B. J., Kersters K., Goossens H., Moss C. W. Chemotaxonomic analyses of Bacteroides gracilis and Bacteroides ureolyticus and reclassification of B. gracilis as Campylobacter gracilis comb. nov. Int J Syst Bacteriol. 1995 Jan;45(1):145–152. doi: 10.1099/00207713-45-1-145. [DOI] [PubMed] [Google Scholar]
  156. Vandamme P., Falsen E., Pot B., Hoste B., Kersters K., De Ley J. Identification of EF group 22 campylobacters from gastroenteritis cases as Campylobacter concisus. J Clin Microbiol. 1989 Aug;27(8):1775–1781. doi: 10.1128/jcm.27.8.1775-1781.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  157. Vandamme P., Falsen E., Pot B., Kersters K., De Ley J. Identification of Campylobacter cinaedi isolated from blood and feces of children and adult females. J Clin Microbiol. 1990 May;28(5):1016–1020. doi: 10.1128/jcm.28.5.1016-1020.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  158. Vandamme P., Falsen E., Rossau R., Hoste B., Segers P., Tytgat R., De Ley J. Revision of Campylobacter, Helicobacter, and Wolinella taxonomy: emendation of generic descriptions and proposal of Arcobacter gen. nov. Int J Syst Bacteriol. 1991 Jan;41(1):88–103. doi: 10.1099/00207713-41-1-88. [DOI] [PubMed] [Google Scholar]
  159. Vandamme P., Hommez J., Vancanneyt M., Monsieurs M., Hoste B., Cookson B., Wirsing von König C. H., Kersters K., Blackall P. J. Bordetella hinzii sp. nov., isolated from poultry and humans. Int J Syst Bacteriol. 1995 Jan;45(1):37–45. doi: 10.1099/00207713-45-1-37. [DOI] [PubMed] [Google Scholar]
  160. Vandamme P., Pugina P., Benzi G., Van Etterijck R., Vlaes L., Kersters K., Butzler J. P., Lior H., Lauwers S. Outbreak of recurrent abdominal cramps associated with Arcobacter butzleri in an Italian school. J Clin Microbiol. 1992 Sep;30(9):2335–2337. doi: 10.1128/jcm.30.9.2335-2337.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  161. Vandamme P., Vancanneyt M., Pot B., Mels L., Hoste B., Dewettinck D., Vlaes L., van den Borre C., Higgins R., Hommez J. Polyphasic taxonomic study of the emended genus Arcobacter with Arcobacter butzleri comb. nov. and Arcobacter skirrowii sp. nov., an aerotolerant bacterium isolated from veterinary specimens. Int J Syst Bacteriol. 1992 Jul;42(3):344–356. doi: 10.1099/00207713-42-3-344. [DOI] [PubMed] [Google Scholar]
  162. Vaneechoutte M., Rossau R., De Vos P., Gillis M., Janssens D., Paepe N., De Rouck A., Fiers T., Claeys G., Kersters K. Rapid identification of bacteria of the Comamonadaceae with amplified ribosomal DNA-restriction analysis (ARDRA). FEMS Microbiol Lett. 1992 Jun 15;72(3):227–233. doi: 10.1111/j.1574-6968.1992.tb05102.x. [DOI] [PubMed] [Google Scholar]
  163. Vera Cruz C. M., Gosselé F., Kersters K., Segers P., Van den Mooter M., Swings J., De Ley J. Differentiation between Xanthomonas campestris pv. oryzae, Xanthomonas campestris pv. oryzicola and the bacterial 'brown blotch' pathogen on rice by numerical analysis of phenotypic features and protein gel electrophoregrams. J Gen Microbiol. 1984 Nov;130(11):2983–2999. doi: 10.1099/00221287-130-11-2983. [DOI] [PubMed] [Google Scholar]
  164. Versalovic J., Koeuth T., Lupski J. R. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res. 1991 Dec 25;19(24):6823–6831. doi: 10.1093/nar/19.24.6823. [DOI] [PMC free article] [PubMed] [Google Scholar]
  165. Viale A. M., Arakaki A. K., Soncini F. C., Ferreyra R. G. Evolutionary relationships among eubacterial groups as inferred from GroEL (chaperonin) sequence comparisons. Int J Syst Bacteriol. 1994 Jul;44(3):527–533. doi: 10.1099/00207713-44-3-527. [DOI] [PubMed] [Google Scholar]
  166. Vogel R. F., Böcker G., Stolz P., Ehrmann M., Fanta D., Ludwig W., Pot B., Kersters K., Schleifer K. H., Hammes W. P. Identification of lactobacilli from sourdough and description of Lactobacillus pontis sp. nov. Int J Syst Bacteriol. 1994 Apr;44(2):223–229. doi: 10.1099/00207713-44-2-223. [DOI] [PubMed] [Google Scholar]
  167. Welch D. F. Applications of cellular fatty acid analysis. Clin Microbiol Rev. 1991 Oct;4(4):422–438. doi: 10.1128/cmr.4.4.422. [DOI] [PMC free article] [PubMed] [Google Scholar]
  168. Welsh J., McClelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res. 1990 Dec 25;18(24):7213–7218. doi: 10.1093/nar/18.24.7213. [DOI] [PMC free article] [PubMed] [Google Scholar]
  169. Welsh J., McClelland M. PCR-amplified length polymorphisms in tRNA intergenic spacers for categorizing staphylococci. Mol Microbiol. 1992 Jun;6(12):1673–1680. doi: 10.1111/j.1365-2958.1992.tb00892.x. [DOI] [PubMed] [Google Scholar]
  170. Wesley I. V., Wesley R. D., Cardella M., Dewhirst F. E., Paster B. J. Oligodeoxynucleotide probes for Campylobacter fetus and Campylobacter hyointestinalis based on 16S rRNA sequences. J Clin Microbiol. 1991 Sep;29(9):1812–1817. doi: 10.1128/jcm.29.9.1812-1817.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  171. Weyant R. S., Hollis D. G., Weaver R. E., Amin M. F., Steigerwalt A. G., O'Connor S. P., Whitney A. M., Daneshvar M. I., Moss C. W., Brenner D. J. Bordetella holmesii sp. nov., a new gram-negative species associated with septicemia. J Clin Microbiol. 1995 Jan;33(1):1–7. doi: 10.1128/jcm.33.1.1-7.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  172. Whitaker R. J., Byng G. S., Gherna R. L., Jensen R. A. Comparative allostery of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase as an indicator of taxonomic relatedness in pseudomonad genera. J Bacteriol. 1981 Feb;145(2):752–759. doi: 10.1128/jb.145.2.752-759.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  173. Willems A., Collins M. D. Phylogenetic analysis of rhizobia and agrobacteria based on 16S rRNA gene sequences. Int J Syst Bacteriol. 1993 Apr;43(2):305–313. doi: 10.1099/00207713-43-2-305. [DOI] [PubMed] [Google Scholar]
  174. Willems A., Falsen E., Pot B., Jantzen E., Hoste B., Vandamme P., Gillis M., Kersters K., De Ley J. Acidovorax, a new genus for Pseudomonas facilis, Pseudomonas delafieldii, E. Falsen (EF) group 13, EF group 16, and several clinical isolates, with the species Acidovorax facilis comb. nov., Acidovorax delafieldii comb. nov., and Acidovorax temperans sp. nov. Int J Syst Bacteriol. 1990 Oct;40(4):384–398. doi: 10.1099/00207713-40-4-384. [DOI] [PubMed] [Google Scholar]
  175. Willems A., Goor M., Thielemans S., Gillis M., Kersters K., De Ley J. Transfer of several phytopathogenic Pseudomonas species to Acidovorax as Acidovorax avenae subsp. avenae subsp. nov., comb. nov., Acidovorax avenae subsp. citrulli, Acidovorax avenae subsp. cattleyae, and Acidovorax konjaci. Int J Syst Bacteriol. 1992 Jan;42(1):107–119. doi: 10.1099/00207713-42-1-107. [DOI] [PubMed] [Google Scholar]
  176. Williams J. G., Kubelik A. R., Livak K. J., Rafalski J. A., Tingey S. V. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 1990 Nov 25;18(22):6531–6535. doi: 10.1093/nar/18.22.6531. [DOI] [PMC free article] [PubMed] [Google Scholar]
  177. Woese C. R. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. doi: 10.1128/mr.51.2.221-271.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  178. Wolters J., Erdmann V. A. Compilation of 5S rRNA and 5S rRNA gene sequences. Nucleic Acids Res. 1988;16 (Suppl):r1–70. doi: 10.1093/nar/16.suppl.r1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  179. Wyss C. Campylobacter-Wolinella group organisms are the only oral bacteria that form arylsulfatase-active colonies on a synthetic indicator medium. Infect Immun. 1989 May;57(5):1380–1383. doi: 10.1128/iai.57.5.1380-1383.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  180. Yabuuchi E., Kosako Y., Oyaizu H., Yano I., Hotta H., Hashimoto Y., Ezaki T., Arakawa M. Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiol Immunol. 1992;36(12):1251–1275. doi: 10.1111/j.1348-0421.1992.tb02129.x. [DOI] [PubMed] [Google Scholar]
  181. Zillig W., Klenk H. P., Palm P., Pühler G., Gropp F., Garrett R. A., Leffers H. The phylogenetic relations of DNA-dependent RNA polymerases of archaebacteria, eukaryotes, and eubacteria. Can J Microbiol. 1989 Jan;35(1):73–80. doi: 10.1139/m89-011. [DOI] [PubMed] [Google Scholar]
  182. de Weger L. A., Jann B., Jann K., Lugtenberg B. Lipopolysaccharides of Pseudomonas spp. that stimulate plant growth: composition and use for strain identification. J Bacteriol. 1987 Apr;169(4):1441–1446. doi: 10.1128/jb.169.4.1441-1446.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  183. van Belkum A. DNA fingerprinting of medically important microorganisms by use of PCR. Clin Microbiol Rev. 1994 Apr;7(2):174–184. doi: 10.1128/cmr.7.2.174. [DOI] [PMC free article] [PubMed] [Google Scholar]