1887

Abstract

All living organisms fall into discrete clusters of closely related individuals on the basis of gene sequence similarity. Evolutionary genetic theory predicts that in the bacterial world, each sequence similarity cluster should correspond to an ecologically distinct population. Indeed, surveys of sequence diversity in protein-coding genes show that sequence clusters correspond to ecological populations. Future population surveys of protein-coding gene sequences can be expected to disclose many previously unknown ecological populations of bacteria. Sequence similarity clustering in protein-coding genes is recommended as a primary criterion for demarcating taxa.

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1997-10-01
2024-04-20
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References

  1. Ambler R. P. 1996; The distance between bacterial species in sequence space. J. Mol. Evol. 42:617–630
    [Google Scholar]
  2. Ash C., Farrow J. A. E., Dorsch M., Stackebrandt E., Collins M. D. 1991; Comparative analysis of Bacillus anthracis, Bacillus cereus, and related species on the basis of reverse transcriptase sequencing of 16S rRNA. Int. J. Syst. Bacteriol. 41:343–346
    [Google Scholar]
  3. Ash C., Farrow J. A. E., Wallbanks S., Collins M. D. 1991; Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small subunit ribosomal RNA sequences. Lett. Appl. Microbiol. 13:202–206
    [Google Scholar]
  4. Atwood K. C., Schneider L. K., Ryan F. J. 1951; Periodic selection in Escherichia coli. Proc. Natl. Acad. Sci. USA 37:146–155
    [Google Scholar]
  5. Avise J. C. 1994 Molecular markers, natural history and evolution. 104 Chapman and Hall; New York, N.Y.:
    [Google Scholar]
  6. Baess I. 1983; Deoxyribonucleic acid relationships between different serovars of Mycobacterium avium, Mycobacterium intracellulare and Mycobacterium scrofulaceum. Acta Pathol. Microbiol. Immunol. Scand. Sect. B 91:201–203
    [Google Scholar]
  7. Balmelli T., Piffaretti J. 1996; Analysis of the genetic polymorphism of Borrelia burgdorferi sensu lato by multilocus enzyme electrophoresis. Int. J. Syst. Bacteriol. 46:167–172
    [Google Scholar]
  8. Baranton G., Postic D., Saint Girons I., Boerlin P., Piffaretti J. C., Assous M., Grimont P. A. 1992; Delineation of Borrelia burgdorferi sensu stricto, Borrelia garinii sp. nov., and group VS461 associated with Lyme borreliosis. Int. J. Syst. Bacteriol. 42:378–383
    [Google Scholar]
  9. Boddinghaus B., Wolters J., Heikens W., Bottger E. C. 1990; Phylogenetic analysis and identification of different serovars of Mycobacterium intracellulare at the molecular level. FEMS Microbiol. Lett. 70:197–204
    [Google Scholar]
  10. Bonnet F., Saillard C., Bove J. M., Leach R. H., Rose D. L., Cottew G. S., Tulley J. G. 1993; DNA relatedness between field isolates of mycoplasma F38 group, the agent of contagious caprine pleuropneumonia, and strains of Mycoplasma capricolum. Int. J. Syst. Bacteriol. 43:597–602
    [Google Scholar]
  11. Boyd E. F., Nelson K., Wang F., Whittam T. S., Selander R. K. 1994; Molecular genetic basis of allelic polymorphism in malate dehydrogenase (mdh) in natural populations of Escherichia coli and Salmonella enterica. Proc. Natl. Acad. Sci. USA 91:1280–1284
    [Google Scholar]
  12. Boyd E. F., Wang F., Whittam T. S., Selander R. K. 1996; Molecular genetic relationships of the salmonellae. Appl. Environ. Microbiol. 62:804–808
    [Google Scholar]
  13. Britschgi T. B., Giovannoni S. J. 1991; Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing. Appl. Environ. Microbiol. 57:1707–1713
    [Google Scholar]
  14. Cohan F. M. 1994; The effects of rare but promiscuous genetic exchange on evolutionary divergence in prokaryotes. Am. Nat. 143:965–986
    [Google Scholar]
  15. Cohan F. M. 1994; Genetic exchange and evolutionary divergence in prokaryotes. Trends Ecol. Evol. 9:175–180
    [Google Scholar]
  16. Cohan F. M. 1995; Does recombination constrain neutral divergence among bacterial taxa?. Evolution 49:164–175
    [Google Scholar]
  17. Cohan F. M. 1996; The role of genetic exchange in bacterial evolution. ASM News 62:631–636
    [Google Scholar]
  18. Cohan F. M. Genetic structure of bacterial populations. Singh R., Krimbas C.ed Evolutionary genetics from molecules to morphology, in press Cambridge University Press; Cambridge, England.:
    [Google Scholar]
  19. Cohan F. M., Roberts M. S., King E. C. 1991; The potential for genetic exchange by transformation within a natural population of Bacillus subtilis. Evolution 45:1393–1421
    [Google Scholar]
  20. Collins M. D., Williams A. M., Wallbanks S. 1990; The phylogeny of Aerococcus and Pediococcus as determined by 16S rRNA sequence analysis: description of Tetragenococcus gen. nov. FEMS Microbiol. Lett. 70:255–262
    [Google Scholar]
  21. Darrasse A., Priou S., Kotoujansky A., Bertheau Y. 1994; PCR and restriction fragment length polymorphism of a pel gene as a tool to identify Erwinia carotovora in relation to potato diseases. Appl. Environ. Microbiol. 60:1437–1443
    [Google Scholar]
  22. Dobson S. J., McMeekin T. A., Franzmann P. D. 1993; Phylogenetic relationships between some members of the genera Deleya, Halomonas, and Halovibrio. Int. J. Syst. Bacteriol. 43:665–673
    [Google Scholar]
  23. Dolina M., Peduzzi R. 1993; Population genetics of human, animal and environmental Yersinia strains. Appl. Environ. Microbiol. 59:442–450
    [Google Scholar]
  24. Drake J. W. 1991; A constant rate of spontaneous mutation in DNA-based microbes. Proc. Natl. Acad. Sci. USA 88:7160–7164
    [Google Scholar]
  25. Foreman M., Sandstrom G., Sjostedt A. 1994; Analysis of 16S ribosomal DNA sequences of Francisella strains and utilization for determination of the phylogeny of the genus and for identification of strains by PCR. Int. J. Syst. Bacteriol. 44:38–46
    [Google Scholar]
  26. Fox G. E., Wisotzkey J. D., Jurtshuk P. Jr. 1992; How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacteriol. 42:166–170
    [Google Scholar]
  27. Fukunaga M., Koreki Y. 1996; A phylogenetic analysis of Borrelia burgdorferi sensu lato isolates associated with Lyme disease in Japan by flagellin gene sequence determination. Int. J. Syst. Bacteriol. 46:416–421
    [Google Scholar]
  28. Gordon R. E., Haynes W. C., Pang C. H.-N. 1973 The genus Bacillus. Agricultural handbook no. 427 U.S. Department of Agriculture; Washington, D.C.:
    [Google Scholar]
  29. Guibourdenche M., Popoff M. Y., Riou J. Y. 1986; Deoxyribonucleic acid relatedness among Neisseria gonorrhoeae, N. meningitidis, N. lactamica, N. cinerea and “Neisseria polysaccharea.”. Ann. Inst. Pasteur Microbiol 137B:2177–185
    [Google Scholar]
  30. Gundersen D. E., Lee I.-M., Schaff D. A., Harrison N. A., Chang C. J., Davis R. E., Kingsbury D. T. 1996; Genomic diversity and differentiation among phytoplasma strains in 16S rRNA groups I (aster yellows and related phytoplasmas) and III (X-disease and related phytoplasmas). Int. J. Syst. Bacteriol. 46:64–75
    [Google Scholar]
  31. Guttman D. S., Dykhuizen D. E. 1994; Clonal divergence in Escherichia coli is a result of recombination, not mutation. Science 266:1380–1383
    [Google Scholar]
  32. Henderson I., Duggleby C. J., Turnbull P. C. 1994; Differentiation of Bacillus anthracis from other Bacillus cereus group bacteria with the PCR. Int. J. Syst. Bacteriol. 44:99–105
    [Google Scholar]
  33. Heyndrickx M., Vandemeulebroecke K., Hoste B., Janssen P., Kersters K., De Vos P., Logan N. A., Ali N., Berkeley R. C. W. 1996; Reclassification of Paenibacillus (formerly Bacillus) pulvifaciens (Nakamura 1984) Ash et al. 1994, a later subjective synonym of Paenibacillus (formerly Bacillus) larvae (White 1906) Ash et al. 1994, as a subspecies of P. larvae, with emended descriptions of P. larvae as P. larvae subsp. larvae and P. larvae subsp. pulvifaciens. Int. J. Syst. Bacteriol. 46:270–279
    [Google Scholar]
  34. Hudson R. R. 1987; Estimating the recombination parameter of a finite population model without selection. Genet. Res. 50:242–250
    [Google Scholar]
  35. Ichige A., Walker G. C. 1997; Genetic analysis of the Rhizobium meliloti bacA gene: functional interchangeability with the Escherichia coli sbmA gene and phenotypes of mutants. J. Bacteriol. 179:209–216
    [Google Scholar]
  36. Johnson J. L. 1986 Nucleic acids in bacterial classification. 972–975 Sneath P. H. A., Mair N. S., Sharpe N. E., Holt J. G.ed Bergey’s manual of systematic bacteriology 2 Williams & Wilkins; Baltimore, Md.:
    [Google Scholar]
  37. Kapur V., Li L. L., Hamrick M. R., Plikaytis B. B., Shinnick T. M., Telenti A., Jacobs W. R. Jr., Banerjee A., Cole S., Yuen K. Y. 1995; Rapid Mycobacterium species assignment and unambiguous identification of mutations associated with antimicrobial resistance in Mycobacterium tuberculosis by automated DNA sequencing. Arch. Pathol. Lab. Med. 119:131–138
    [Google Scholar]
  38. Karaolis D. K. R., Lan R., Reeves P. K. 1995; The sixth and seventh cholera pandemics are due to independent clones separately derived from environmental, nontoxigenic, non-Ol Vibrio cholerae. J. Bacteriol. 177:3191–3198
    [Google Scholar]
  39. Keis S., Bennet C. F., Ward V. K., Jones D. T. 1995; Taxonomy and phylogeny of industrial solvent-producing Clostridia. Int. J. Syst. Bacteriol. 45:693–705
    [Google Scholar]
  40. Kimura M. 1983 The neutral theory of molecular evolution. Cambridge University Press; Cambridge, England.:
    [Google Scholar]
  41. Knight I. T., Holben W. E., Tiedje J. M., Colwell R. R. 1992 Nucleic acid hybridization techniques for detection, identification, and enumeration of microorganisms in the environment. 65–91 Levin M. A., Seidler R. J., Rogul M.ed Microbial ecology: principles, methods, and applications McGraw-Hill; New York, N.Y.:
    [Google Scholar]
  42. Koch A. L. 1974; The pertinence of the periodic selection phenomenon to prokaryotic evolution. Genetics 77:127–142
    [Google Scholar]
  43. Lan R., Reeves P. R. 1996; Gene transfer is a major factor in bacterial evolution. Mol. Biol. Evol. 13:47–55
    [Google Scholar]
  44. Larkin J. M., Stokes J. L. 1967; Taxonomy of psychrophilic strains of Bacillus. J. Bacteriol. 94:889–895
    [Google Scholar]
  45. Legard D. E., Aquadro C. F., Hunter J. E. 1993; DNA sequence variation and phylogenetic relationships among strains of Pseudomonas syringae pv. syringae inferred from restriction site maps and restriction fragment length polymorphism. Appl. Environ. Microbiol. 59:4180–4188
    [Google Scholar]
  46. Levin B. R. 1981; Periodic selection, infectious gene exchange and the genetic structure of E. coli populations. Genetics 99:1–23
    [Google Scholar]
  47. Love D. N. 1995; Porphyromonas macacae comb, nov., a consequence of Bacteroides macacae being a senior synonym of Porphyromonas salivosa. Int. J. Syst. Bacteriol. 45:90–92
    [Google Scholar]
  48. Mallet J. 1995; A species definition for the modern synthesis. Trends Ecol. Evol. 10:294–299
    [Google Scholar]
  49. Martinez E., Romero D., Palacios P. 1990; The Rhizobium genome. Crit. Rev. Plant Sci. 9:17–19
    [Google Scholar]
  50. Maynard Smith J., Smith N. H., O’Rourke M., Spratt B. G. 1993; How clonal are bacteria? Proc. Natl. Acad. Sci. USA 90:4384–4388
    [Google Scholar]
  51. Mikulskis A. V., Cornelis G. R. 1994; A new class of proteins regulating gene expression in enterobacteria. Mol. Microbiol. 11:77–86
    [Google Scholar]
  52. Milkman R., Bridges M. M. 1993; Molecular evolution of the Escherichia coli chromosome. Genetics 133:455–468
    [Google Scholar]
  53. Murray R. G. E., Stackebrandt E. 1995; Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes. Int. J. Syst. Bacteriol. 45:186–187
    [Google Scholar]
  54. Nakamura L. K. 1984; Bacilluspsychrophilus sp. nov., nom. rev. Int. J. Syst. Bacteriol. 34:121–123
    [Google Scholar]
  55. Nakamura L. K. 1990; Bacillus thiaminolyticus sp. nov., nom. rev. Int. J. Syst. Bacteriol. 40:242–246
    [Google Scholar]
  56. Nakamura L. K. 1994; DNA relatedness among Bacillus thuringiensis serovars. Int. J. Syst. Bacteriol. 44:125–129
    [Google Scholar]
  57. Nei M. 1987 Molecular evolutionary genetics. Columbia University Press; New York, N.Y.:
    [Google Scholar]
  58. Nelson K., Selander R. K. 1992; Evolutionaiy genetics of the proline permease gene (putP) and the control region of the proline utilization operon in populations of Salmonella and Escherichia coli. J. Bacteriol. 174:6886–6895
    [Google Scholar]
  59. Nelson K., Selander R. K. 1994; Intergenic transfer and recombination of the 6-phosphogluconate dehydrogenase gene (gnd) in enteric bacteria. Proc. Natl. Acad. Sci. USA 91:10227–10231
    [Google Scholar]
  60. Nelson K., Whittam T. S., Selander R. K. 1991; Nucleotide polymorphism and evolution in the glyceraldehyde-3-phosphate dehydrogenase gene (gapA) in natural populations of Salmonella and Escherichia coli. Proc. Natl. Acad. Sci. USA 88:6667–6671
    [Google Scholar]
  61. Nicholson L. A., Morrow C. J., Comer L. A., Hodgson A. L. M. 1994; Phylogenetic relationship of Fusobacterium necrophorum A, AB, and B biotypes based upon 16S rRNA gene sequence analysis. Int. J. Syst. Bacteriol. 44:315–319
    [Google Scholar]
  62. Normand P., Orso S., Cournoyer B., Jeannin P., Chapelon C., Dawson J., Evtushenko L., Misra A. K. 1996; Molecular phylogeny of the genus Frankia and related genera and emendation of the family Frankiaceae. Int. J. Syst. Bacteriol. 46:1–9
    [Google Scholar]
  63. Osuna R., Boylan S. A., Bender R. A. 1991; In vitro transcription of the histidine utilization (hutUH) operon from Klebsiella aerogenes. J. Bacteriol. 173:116–123
    [Google Scholar]
  64. Palys T., Berger E., Nakamura L. K., Cohan F. M. Unpublished data
  65. Poveda J. B., Giebel J., Flossdorf J., Meier J., Kirchhoff H. 1994; Mycoplasma buteonis sp. nov., Mycoplasma falconis sp. nov., and Mycoplasma gypis sp. nov., three species from birds of prey. Int. J. Syst. Bacteriol. 44:94–98
    [Google Scholar]
  66. Rainey F. A., Weiss N., Stackebrandt E. 1995; Phylogenetic analysis of the genera Cellulomonas, Promicromonospora, and Jonesia and the proposal to exclude the genus Jonesia from the family Cellulomonadaceae. Int. J. Syst. Bacteriol. 45:649–652
    [Google Scholar]
  67. Rasmussen F. O., Skouboe P., Dons L., Rossen L., Olson J. E. 1995; Listeria monocytogenes exists in at least three evolutionary lines: evidence from flagellin, invasive associated protein and listeriolysin O genes. Microbiology 141:2053–2061
    [Google Scholar]
  68. Rayssiguier C., Thaler D. S., Radman M. 1989; The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature 342:396–401
    [Google Scholar]
  69. Roberts M. S., Cohan F. M. 1995; Recombination and migration rates in natural populations of Bacillus subtilis and Bacillus mojavensis. Evolution 49:1081–1094
    [Google Scholar]
  70. Roberts M. S., Nakamura L. K., Cohan F. M. 1994; Bacillus mojavensis sp. nov., distinguishable from Bacillus subtilis by sexual isolation, divergence in DNA sequence, and differences in fatty acid composition. Int. J. Syst. Bacteriol. 44:256–264
    [Google Scholar]
  71. Roberts M. S., Nakamura L. K., Cohan F. M. 1996; Bacillus vallismortis sp. nov., a close relative of Bacillus subtilis, isolated from soil in Death Valley, California. Int. J. Syst. Bacteriol. 46:470–475
    [Google Scholar]
  72. Ros C., Belak K. 1996; Detection and identification of mycobacteria in formalin-fixed, paraffin-embedded tissues by nested PCR and restriction enzyme analysis. J. Clin. Microbiol. 34:2351–2355
    [Google Scholar]
  73. Sedgwick S. G., Lodwick D., Doyle N., Crowne H., Strike P. 1991; Functional complementation between chromosomal and plasmid mutagenic DNA repair genes in bacteria. Mol. Gen. Genet. 229:428–436
    [Google Scholar]
  74. Segovia L., Pinero D., Palacios R., Martinez-Romero E. 1991; Genetic structure of a soil population of nonsymbiotic Rhizobium leguminosarum. Appl. Environ. Microbiol. 57:426–433
    [Google Scholar]
  75. Selander R. K., Musser J. M. 1990 Population genetics of bacterial pathogenesis. 11–36 Iglewski B. H., Clark V. L.ed molecular basis of bacterial pathogenesis Academic Press; San Diego, Calif.:
    [Google Scholar]
  76. Sharp P. M., Nolan N. C., Cholmain N. N., Devine K. M. 1992; DNA sequence variability at the rplX locus of Bacillus subtilis. J. Gen. Microbiol. 138:39–45
    [Google Scholar]
  77. Smart C. D., Schneider B., Blomquist C. L., Guerra L. J., Harrison N. A., Ahrens U., Lorenz K. H., Seemuller E., Kirkpatrick B. C. 1996; Phytoplasma-specific PCR primers based on sequences of the 16S-23S rRNA spacer region. Appl. Environ. Microbiol. 62:2988–2993
    [Google Scholar]
  78. Soini H., Bottger E. C., Viljanen M. K. 1994; Identification of mycobacteria by PCR-based sequence determination of the 32-kilodalton protein gene. J. Clin. Microbiol. 32:2944–2947
    [Google Scholar]
  79. Soria G., Barbe J., Gibert I. 1994; Molecular fingerprinting of Salmonella typhimurium by IS200-typing as a tool for epidemiological and evolutionary studies. Microbiologia 10:57–68
    [Google Scholar]
  80. Taghavi M., Hayward C., Sly L. I., Fegan M. 1996; Analysis of the phylogenetic relationships of the strains of Burkholderia solanacearum, Pseudomonas syzygii, the blood disease bacterium of banana based on 16S rRNA gene sequences. Int. J. Syst. Bacteriol. 46:10–15
    [Google Scholar]
  81. Thampapillai R. Lan, Reeves P. R. 1994; Molecular evolution in the gnd locus of Salmonella enterica. Mol. Biol. Evol. 11:813–828
    [Google Scholar]
  82. Vandamme P., Pot B., Gillis M., De Vos P., Kersters K., Swings J. 1996; Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60:407–438
    [Google Scholar]
  83. Vauterin L., Hoste B., Kersters K., Swings J. 1995; Reclassification of Xanthomonas. Int. J. Syst. Bacteriol. 45:472–489
    [Google Scholar]
  84. Vazquez J. A., de la Fuente L., Berron S., O’Rourke M., Smith N. H., Zhou J., Spratt B. G. 1993; Ecological separation and genetic isolation of Neisseria gonorrhoeae and Neisseria meningitidis. Curr. Biol. 3:567–572
    [Google Scholar]
  85. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E., Stackebrandt E., Starr M. P., Triiper H. G. 1987; Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37:463–464
    [Google Scholar]
  86. Whittam T. S., Ake S. E. 1993 Genetic polymorphisms and recombination in natural populations of Escherichia coli. 223–245 Takahata N., Clark A. G.ed Molecular paleopopulation biology Japan Scientific Society Press; Tokyo, Japan.:
    [Google Scholar]
  87. Williams A. M., Rodriguez U. M., Collins M. D. 1991; Intrageneric relationships of Enterococci as determined by reverse transcriptase sequencing of small-subunit rRNA. Res. Microbiol. 142:67–74
    [Google Scholar]
  88. Woese C. R. 1987; Bacterial evolution. Microbiol. Rev. 51:221–271
    [Google Scholar]
  89. Yu H., Schurr M. J., Deretic V. 1995; Functional equivalence of Escherichia coli <rE and Pseudomonas aeruginosa AlgU: E. coli rpoE restores mucoidy and reduces sensitivity to reactive oxygen intermediates in algU mutants of P. aeruginosa. J. Bacteriol. 177:3259–3268
    [Google Scholar]
  90. Zawadzki P., Roberts M. S., Cohan F. M. 1995; The log-linear relationship between sexual isolation and sequence divergence in Bacillus transformation is robust. Genetics 140:917–932
    [Google Scholar]
  91. Zhou J., Spratt B. G. 1992; Sequence diversity within the argF,fbp and recA genes of natural isolates of Neisseria meningitidis: interspecies recombination within the argF gene. Mol. Microbiol. 6:2135–2146
    [Google Scholar]
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