What are bacterial species?

Annual Review of Microbiology

Volumn 56, Issue , 2002, Pages 457-487

  Cohan, Frederick M ^a  

^a WESLEYAN UNIVERSITY   (United States)

Author keywords

Ecotype; Genetic exchange; MLST; Speciation; Species concept; Systematics

Indexed keywords

BACTERIAL DNA;

BACTERIOLOGY; BACTERIUM; BACTERIUM ADHERENCE; BIODIVERSITY; DNA SEQUENCE; ECOLOGY; EUKARYOTE; GENE CLUSTER; GENE SEQUENCE; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; REVIEW; SEQUENCE ANALYSIS; SPECIES DIFFERENCE;

BACTERIA; CLUSTER ANALYSIS; MULTIGENE FAMILY; PHENOTYPE; PHYLOGENY; SEQUENCE ANALYSIS; SPECIES SPECIFICITY; VARIATION (GENETICS);

BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 0036407157     PISSN: 00664227     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.micro.56.012302.160634     Document Type: Review

References (110)

1. Achtman M, van der Ende A, Zhu P, Koroleva IS, Kusucek B, et al. 2001. Molecular epidemiology of serogroup A meningitis in Moscow, 1969 to 1997. Emerg. Infect. Dis. 7:420-27
2. Akopyants NS, Fradkov A, Diatchenko L, Hill JE, Siebert PD, et al. 1998. PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori. Proc. Natl. Acad. Sci. USA 95:13108-13
3. Alm RA, Ling LL, Moir DT, King BL, Brown ED, et al. 1999. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397:176-80
4. American Society for Microbiology. 1957. Bergey's Manual of Determinative Bacteriology. Baltimore: Williams & Wilkins. 7th ed.
5. Atwood KC, Schneider LK, Ryan FJ. 1951. Periodic selection in Escherichia coli. Proc. Natl. Acad. Sci. USA 37:146-55
6. Avise JC. 2000. Phylogeography: The History and Formation of Species. Cambridge, MA: Harvard Univ. Press
7. Balmelli T, Piffaretti J. 1996. Analysis of the genetic polymorphism of Borrelia burgdorferi sensu lato by multilocus enzyme electrophoresis. Int. J. Syst. Bacteriol. 46:167-72
8. Baranton G, Postic D, Saint Girons I, Boerlin P, Piffaretti JC, et al. 1992. Delineation of Borrelia burgdorferi sensu stricto, Borrelia garinii sp. nov., and group VS461 associated with Lyme borreliosis. Int. J. Syst. Bacteriol. 42:378-83
9. Barrett SJ, Sneath PH. 1994. A numerical phenotypic taxonomic study of the genus Neisseria. Microbiology 140:2867-91
10. Bochner BR. 1989. Sleuthing out bacterial identities. Nature 339:157-58
11. Bush GL. 1994. Sympatric speciation in animals: New wine in old bottles. Trends Ecol. Evol. 9:285-88
12. Chan MS, Maiden MC, Spratt BG. 2001. Database-driven multi locus sequence typing (MLST) of bacterial pathogens. Bioinformatics 17:1077-83
13. Cohan FM. 1994. Genetic exchange and evolutionary divergence in prokaryotes. Trends in Ecol. Evol. 9:175-80
14. Cohan FM. 1994. The effects of rare but promiscuous genetic exchange on evolutionary divergence in prokaryotes. Am. Nat. 143:965-86
15. Cohan FM. 1996. The role of genetic exchange in bacterial evolution. ASM News 62:631-36
16. Cohan FM. 2001. Bacterial species and speciation. Syst. Biol. 50:513-24
17. Cohan FM. 2002. Clonal structure: An overview. In Encyclopedia of Evolution, ed. M Pagel, pp. 159-61. Oxford: Oxford Univ. Press
18. Cohan FM, Roberts MS, King EC. 1991. The potential for genetic exchange by transformation within a natural population of Bacillus subtilis. Evolution 45:1393-421
19. DeLong E, Pace N. 2001. Environmental diversity of Bacteria and Archaea. Syst. Biol. 50:470-78
20. de Queiroz K. 1998. The general lineage concept of species, species criteria, and the process of speciation. In Endless Forms: Species and Speciation, ed. DJ Howard, SH Berlocher, pp 57-75. Oxford: Oxford Univ. Press
21. Dojka MA, Harris JK, Pace NR. 2000. Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of Bacteria. Appl. Environ. Microbiol. 66:1617-21
22. Duncan KE, Istock CA, Graham JB, Ferguson N. 1989. Genetic exchange between Bacillus subtilis and Bacillus licheniformis: Variable hybrid stability and the nature of species. Evolution 43:1585-609
23. Dykhuizen DE. 1998. Santa Rosalia revisited: Why are there so many species of bacteria? Antonie Van Leeuwenhoek 73:25-33
24. Dykhuizen DE, Green L. 1991. Recombination in Escherichia coli and the definition of biological species. J. Bacteriol. 173:7257-68
25. Edwards RA, Helm RA, Maloy SR. 1999. Increasing DNA transfer efficiency by temporary inactivation of host restriction. Biotechniques 26:892-98
26. Eldredge N. 1985. Unfinished Synthesis: Biological Hierarchies and Modern Evolutionary Thought. New York: Oxford Univ. Press
27. Enright MC, Spratt BG, Kalia A, Cross JH, Bessen DE. 2001. Multilocus sequence typing of Streptococcus pyogenes and the relationships between emm type and clone. Infect. Immun. 69:2416-27
28. Feil EJ, Maiden MC, Achtman M, Spratt BG. 1999. The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis. Mol. Biol. Evol. 16:1496-502
29. Feil EJ, Smith JM, Enright MC, Spratt BG. 2000. Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data. Genetics 154:1439-50
30. Ferea TL, Botstein D, Brown PO, Rosenzweig RF. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. USA 96:9721-26
31. Futuyma DJ. 1987. On the role of species in anagenesis. Am. Nat. 130:465-73
32. Gause GF. 1934. The Struggle for Existence. Baltimore: Williams & Wilkins
33. Goodfellow M, Manfio GP, Chun J. 1997. Towards a practical species concept for cultivable bacteria. In Species: The Units of Biodiversity, ed. MF Claridge, HA Dawah, MR Wilson, pp 25-29. London: Chapman & Hall
34. Groisman EA, Ochman H. 1997. How Salmonella became a pathogen. Trends Microbiol. 5:343-49
35. Hamilton CM, Aldea M, Washburn BK, Babitzke P, Kushner SR. 1989. New method for generating deletions and gene replacements in Escherichia coli. J. Bacteriol. 171:4617-22
36. Hennig W. 1966. Phylogenetic Systematics. Urbana: Univ. Illinois Press
37. Henriques Normark B, Kalin M, Ortqvist A, Akerlund T, Liljequist BO, et al. 2001. Dynamics of penicillin-susceptible clones in invasive pneumococcal disease. J. Infect. Dis. 184:861-69
38. Hey J, Wakeley J. 1997. A coalescent estimator of the population recombination rate. Genetics 145:833-46
39. Deleted in proof
40. Hudson RR. 1987. Estimating the recombination parameter of a finite population model without selection. Genet. Res. 50:245-50
41. Hudson RR, Kaplan NL. 1985. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111:147-64
42. Hugenholtz PB, Goebel M, Pace NR. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765-74
43. Deleted in text
44. Imhof M, Schlotterer C. 2001. Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc. Natl. Acad. Sci. USA 98:1113-17
45. Johnson JL. 1973. Use of nucleic-acid homologies in the taxonomy of anaerobic bacteria. Int. J. Syst. Bacteriol. 23:308-15
46. Lai YC, Yang SL, Peng HL, Chang HY. 2000. Identification of genes present specifically in a virulent strain of Klebsiella pneumoniae. Infect. Immun. 68:7149-51
47. Lan R, Reeves PR. 1996. Gene transfer is a major factor in bacterial evolution. Mol. Biol. Evol. 13:47-55
48. Lawrence JG, Ochman H. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95:9413-17
49. Linz B, Schenker M, Zhu P, Achtman M. 2000. Frequent interspecific genetic exchange between commensal Neisseriae and Neisseria meningitidis. Mol. Microbiol. 36:1049-58
50. Logan NA, Berkeley RC. 1984. Identification of Bacillus strains using the API system. J. Gen. Microbiol. 130:1871-82
51. Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE, et al. 1998. Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95:3140-45
52. Majewski J, Cohan FM. 1998. The effect of mismatch repair and heteroduplex formation on sexual isolation in Bacillus. Genetics 148:13-18
53. Majewski J, Cohan FM. 1999. Adapt globally, act locally: The effect of selective sweeps on bacterial sequence diversity. Genetics 152:1459-74
54. Mauchline WS, Keevil CW. 1991. Development of the BIOLOG substrate utilization system for identification of Legionella spp. Appl. Environ. Microbiol. 57:3345-49
55. May RM. 1973. On relationships among various types of population models. Am. Nat. 107:46-57
56. Maynard Smith J, Dowson CG, Spratt BG. 1991. Localized sex in bacteria. Nature 349:29-31
57. Maynard Smith J, Smith NH, O'Rourke M, Spratt BG. 1993. How clonal are bacteria? Proc. Natl. Acad. Sci. USA 90:4384-88
58. Mayr E. 1944. Systematics and the Origin of Species from the Viewpoint of a Zoologist. New York: Columbia Univ. Press
59. Mayr E. 1963. Animal Species and Evolution. Cambridge: Belknap Press/Harvard Univ. Press
60. Mayr E. 1982. The Growth of Biological Thought: Diversity, Evolution, and Inheritance, Chapter 6. Cambridge: Harvard Univ. Press
61. McKane M, Milkman R. 1995. Transduction, restriction and recombination patterns in Escherichia coli. Genetics. 139:35-43
62. Meglitsch PA. 1954. On the nature of species. Syst. Zool. 3:491-503
63. Murray RGE, Stackebrandt E. 1995. Taxonomic note: Implementation of the provisional status Candidatus for incompletely described procaryotes. Int. J. Syst. Bacteriol. 45:186-87
64. Nakamura LK, Roberts MS, Cohan FM. 1999. Relationship of Bacillus subtilis clades associated with strains 168 and W23: A proposal for Bacillus subtilis subsp. subtilis subsp. nov. and Bacillus subtilis subsp. spizizenii subsp. nov. Int. J. Syst. Bacteriol. 49:1211-15
65. Normand P, Orso S, Cournover B, Jeannin P, Chapelon C, et al. 1996. Molecular phylogeny of the genus Frankia and related genera and emendation of the family Frankiaceae. Int. J. Syst. Bacteriol. 46:1-9
66. Ochman H, Lawrence JG, Groisman EA. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304
67. O'Rourke M, Spratt BG. 1994. Further evidence for the non-clonal population structure of Neisseria gonorrhoeae: Extensive genetic diversity within isolates of the same electrophoretic type. Microbiology 140:1285-90
68. Palmisano MM, Nakamura LK, Duncan KE, Istock CA, Cohan FM. 2001. Bacillus sonorensis sp. nov., a close relative of Bacillus licheniformis, isolated from soil in the Sonoran Desert, Arizona. Int. J. Syst. Evol. Microbiol. 51:16717-19
69. Palys T, Berger E, Mitrica I, Nakamura LK, Cohan FM. 2000. Protein-coding genes as molecular markers for ecologically distinct populations: The case of two Bacillus species. Int. J. Syst. Evol. Microbiol. 50:1021-28
70. Palys T, Cohan FM, Nakamura LK. 1997. Discovery and classification of ecological diversity in the bacterial world: The role of DNA sequence data. Int. J. Syst. Bacteriol. 47:1145-56
71. Parkhill J, Achtman M, James KD, Bentley SD, Churcher C, et al. 2000. Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature 404:502-6
72. Perna NT, Plunkett G 3rd, Burland V, Mau B, Glasner JD, et al. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529-33
73. Rainey PB, Travisano M. 1998. Adaptive radiation in a heterogeneous environment. Nature 394:69-72
74. Ramsing NB, Ferris MJ, Ward DM. 2000. Highly ordered vertical structure of Synechococcus populations within the onemillimeter-thick photic zone of a hot spring cyanobacterial mat. Appl. Environ. Microbiol. 66:1038-49
75. Rao BJ, Chiu SK, Bazemore LR, Reddy G, Radding CM. 1995. How specific is the first recognition step of homologous recombination? Trends Biochem. Sci. 20:102-13
76. Ravin AW. 1960. The origin of bacterial species: Genetic recombination and factors limiting it between bacterial populations. Bacteriol. Rev. 24:201-20
77. Ravin AW. 1963. Experimental approaches to the study of bacterial phylogeny. Am. Nat. 97:307-18
78. Rayssiguier C, Thaler DS, Radman M. 1989. The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch repair mutants. Nature 342:396-401
79. Read TD, Brunham RC, Shen C, Gill SR, Heidelberg JF, et al. 2000. Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res. 28:1397-406
80. Roberts MS, Cohan FM. 1995. Recombination and migration rates in natural populations of Bacillus subtilis and Bacillus mojavensis. Evolution 49:1081-94
81. Rozen DE, Lenski RE. 2000. Long-term experimental evolution in Escherichia coli. VIII. Dynamics of a balanced polymorphism. Am. Nat. 155:24-35
82. Sasser M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. Tech. Note 101. Microbial ID, Inc., Newark, Del.
83. Selander RK, Musser JM. 1990. Population genetics of bacterial pathogenesis. In Molecular Basis of Bacterial Pathogenesis, ed. BH Iglewski, VL Clark, pp. 11-36. San Diego: Academic
84. Simpson GG. 1961. Principles of Animal Taxonomy. New York: Columbia Univ. Press
85. Slatkin M, Maddison WP. 1989. A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123:603-13
86. Sneath PHA. 1985. Future of numerical taxonomy. In Computer-Assisted Bacterial Systematics, ed. M Goodfellow, D Jones, FG Priest, pp. 415-31. Orlando: Academic
87. Sneath PHA, Sokal RR. 1973. Numerical Taxonomy: The Principles and Practice of Numerical Classification. San Francisco: Freeman
88. Sokal RR, Crovello TJ. 1970. The biological species concept: A critical evaluation. Am. Nat. 104:127-53
89. Stackebrandt E, Goebel BM. 1994. Taxonomic note: A place for DNA:DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846-49
90. Stebbins GL. 1957. Variation and Evolution in Plants. Irvington: Columbia Univ. Press
91. Suerbaum S, Maynard Smith J, Bapumia K, Morelli G, Smith NH, et al. 1998. Free recombination within Helicobacter pylori. Proc. Natl. Acad. Sci. USA 95:12619-24
92. Swofford DL. 1998. Phylogenetic Analysis Using Parsimony (*And Other Methods). Version 4. Sunderland, MA: Sinauer
93. Templeton AR. 1989. The meaning of species and speciation: A genetic perspective. In Speciation and Its Consequences, ed. D Otte, JA Endler, pp. 3-27. Sunderland, MA: Sinauer
94. Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, et al. 2000. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 287:1809-15
95. Trautner TA, Pawlek B, Bron S, Anagnostopoulos C. 1974. Restriction and modification in B. subtilis. Mol. Gen. Genet. 131:181-91
96. Treves DS, Manning S, Adams J. 1998. Repeated evolution of an acetate cross-feeding polymorphism in long-term populations of Escherichia coli. Mol. Biol. Evol. 15:789-97
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 Spanning RJ, Reijnders WN, Stouthamer AH. 1995. Integration of heterologous DNA into the genome of Paracoccus denitrificans is mediated by a family of IS1248-related elements and a second type of integrative recombination event. J. Bacteriol. 177:4772-78
99. Van Valen L. 1976. Ecological species, multispecies, and oaks. Taxon 25:233-39
100. Vulic M, Dionisio F, Taddei F, Radman M. 1997. Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria. Proc. Natl. Acad. Sci. USA 94:9763-67
101. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, et al. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37:463-64
102. White MJD. 1978. Modes of Speciation. San Francisco: Freeman
103. Whittam TS, Ake SE. 1993. Genetic polymorphisms and recombination in natural populations of Escherichia coli. In Molecular Paleopopulation Biology, ed. N Takahata, AG Clark, pp. 223-45. Tokyo: Jpn. Sci. Soc. Press
104. Wiley EO. 1978. The evolutionary species concept reconsidered. Syst. Zool. 27:17-26
105. Woese CR. 2000. Interpreting the universal phylogenetic tree. Proc. Natl. Acad. Sci. USA 97:8392-96
106. Wright S. 1931. Evolution in Mendelian populations. Genetics 16:97-159
107. Young JPW. 1989. The population genetics of bacteria. In Genetics of Bacterial Diversity, ed. DA Hopwood, KF Chater, pp. 417-38. London: Academic
108. Zawadzki P, Cohan FM. 1995. The size and continuity of DNA segments integrated in Bacillus transformation. Genetics 141:1231-43
109. Zhou J, Enright MC, Spratt BG. 2000. Identification of the major Spanish clones of penicillin-resistant pneumococci via the Internet using multilocus sequence typing. J. Clin. Microbiol. 38:977-86
110. Zhu P, van der Ende A, Falush D, Brieske N, Morelli G, et al. 2001. Fit genotypes and escape variants of subgroup III Neisseria meningitidis during three pandemics of epidemic meningitis. Proc. Natl. Acad. Sci. USA 98:5234-39