Prokaryotic systematics in the genomics era

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 101, Issue 1, 2012, Pages 21-34

  Zhi, Xiao Yang ^a   Zhao, Wei ^b,c,d   Li, Wen Jun ^a   Zhao, Guo Ping ^b,c,e,f  

^a YUNNAN UNIVERSITY   (China)

^b INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

^c FUDAN UNIVERSITY   (China)

^d China HYK Gene Technology Company Ltd   (China)

^e CHINESE NATIONAL HUMAN GENOME CENTER AT SHANGHAI   (China)

^f CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Genomics; Molecular phylogeny; Prokaryotic systematics; Taxonomy

Indexed keywords

16S RRNA GENE; BIOINFORMATICS; CONFERENCE PAPER; DNA DNA HYBRIDIZATION; DNA SEQUENCE; FUNCTIONAL GENOMICS; GENE SEQUENCE; GENOME ANALYSIS; GENOMICS; HORIZONTAL GENE TRANSFER; INDEL MUTATION; MOLECULAR PHYLOGENY; MOLECULAR SYSTEMATICS; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; RNA GENE; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENTIATION; TAXONOMIC RANK; TAXONOMY;

ARCHAEA; BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; CHEMISTRY TECHNIQUES, ANALYTICAL; CLASSIFICATION; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; GENOMICS; MICROBIOLOGICAL TECHNIQUES;

PROKARYOTA;

EID: 84856224966     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-011-9667-x     Document Type: Conference Paper

References (138)

1. Achtman M, Wagner M (2008) Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 6:431-440 (Pubitemid 351696437)
2. Andam CP, Gogarten JP (2011) Biased gene transfer in microbial evolution. Nat Rev Microbiol 9:543-555
3. Andam CP, Williams D, Gogarten JP (2010) Biased gene transfer mimics patterns created through shared ancestry. Proc Natl Acad Sci USA 107:10679-10684
4. Andersson JO, Andersson SG (2001) Pseudogenes, junk DNA, and the dynamics of Rickettsia genomes. Mol Biol Evol 18:829-839 (Pubitemid 32372952)
5. Bansal AK, Meyer TE (2002) Evolutionary analysis by wholegenome comparisons. J Bacteriol 184:2260-2272
6. Bapteste E, Susko E, Leigh J, MacLeod D, Charlebois RL, Doolittle WF (2005) Do orthologous gene phylogenies really support tree-thinking? BMC Evol Biol 5:33
7. Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L et al (2009) Prokaryotic evolution and the tree of life are two different things. Biol Direct 4:34
8. Barona-Gómez F, Cruz-Morales P, Noda-García L (2012). What can genome-scale metabolic network reconstructions do for prokaryotic systematics?. Antonie van Leeuwenhoek (in press)
9. Bennett PM (2004) Genome plasticity: insertion sequence elements, transposons and integrons, and DNA rearrangement. Methods Mol Biol 266:71-113
10. Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD et al (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141-147 (Pubitemid 34506788)
11. Beutin L, Miko A, Krause G, Pries K, Haby S, Steege K, Albrecht N (2007) Identification of human-pathogenic strains of Shiga toxin-producing Escherichia coli from food by a combination of serotyping and molecular typing of Shiga toxin genes. Appl Environ Microbiol 73:4769-4775 (Pubitemid 47237224)
12. Bevan RB, Bryant D, Lang BF (2007) Accounting for gene rate heterogeneity in phylogenetic inference. Syst Biol 56:194-205
13. Boussau B, Daubin V (2010) Genomes as documents of evolutionary history. Trends Ecol Evol 25:224-232
14. Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ (2001) Universal trees based on large combined protein sequence data sets. Nat Genet 28:281-285 (Pubitemid 32626033)
15. Buchanan RE (1955) Taxonomy. Annu Rev Microbiol 9:1-20
16. Charlebois RL, Beiko RG, Ragan MA (2003) Microbial phylogenomics: branching out. Nature 421:217
17. Chuang PC, Chen YM, Chen HY, Jou R (2010) Single nucleotide polymorphisms in cell wall biosynthesis-associated genes and phylogeny of Mycobacterium tuberculosis lineages. Infect Genet Evol 10:459-466
18. Coenye T, Vandamme P (2003) Extracting phylogenetic information from whole-genome sequencing projects: the lactic acid bacteria as a test case. Microbiology 149:3507-3517 (Pubitemid 38016678)
19. Coenye T, Gevers D, van de Peer Y, Vandamme P, Swings J (2005) Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev 29:147-167 (Pubitemid 40432465)
20. Cohan FM (2001) Bacterial species and speciation. Syst Biol 50(4):513-524
21. Cohan FM (2002) What are bacterial species? Annu Rev Microbiol 56:457-487 (Pubitemid 35217463)
22. Cohn F (1872) Untersuchungen über Bakterien. Beitr Biol Pflanz 1875 1 (Heft 2):127-224
23. Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, Honore N et al (2001) Massive gene decay in the leprosy bacillus. Nature 409:1007-1011 (Pubitemid 32204045)
24. Colwell RR (1970) Polyphasic taxonomy of bacteria. In: Izuka H, Hasegawa T (eds) Culture collections of microorganisms. University of Tokyo Press, Tokyo, pp 421-436
25. Cui Y, Li Y, Gorge O, Platonov ME, Yan Y, Guo Z, Pourcel C, Dentovskaya SV et al (2008) Insight into microevolution of Yersinia pestis by clustered regularly interspaced short palindromic repeats. PLoS One 3:e2652
26. De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer K-H, Whitman WB (2009) Bergey's Manual of Systematic Bacteriology, 2nd Edn, Vol 3, The Firmacutes, Springer, New York
27. Delsuc F, Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6:361-375 (Pubitemid 40577180)
28. Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284:2124-2129
29. Doolittle WF, Zhaxybayeva O (2009) On the origin of prokaryotic species. Genome Res 19:744-756
30. Dutilh BE, Huynen MA, Bruno WJ, Snel B (2004) The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. J Mol Evol 58:527-539 (Pubitemid 38609888)
31. Dykuizen D, Green L (1991) Recombination in Escherichia coli and the definition of biological species. J Bacteriol 173:7257-7268
32. Eisen JA (1998) Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 8:163-167 (Pubitemid 28177226)
33. Ereshefsky M (2010) Microbiology and the species problem. Biol Philos 25:553-568
34. Farris JS, Källersjö M, Kluge AG, Bult C (1994) Testing the significance of incongruence. Cladistics 10:315-319
35. Fitz-Gibbon ST, House CH (1999) Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res 27:4218-4222 (Pubitemid 29500255)
36. Foster JT, Beckstrom-Sternberg SM, Pearson T, Beckstrom- Sternberg JS, Chain PS et al (2009) Whole-genome-based phylogeny and divergence of the genus Brucella. J Bacteriol 191:2864-2870
37. Gao B, Gupta RS (2012) Microbial Systematics in the Postgenomics Era. Antonie van Leeuwenhoek (in press)
38. Gevers D, Vandepoele K, Simillon C, van de Peer Y (2004) Gene duplication and biased functional retention of paralogs in bacterial genomes. Trends Microbiol 12:148-154 (Pubitemid 38393733)
39. Gil R, Silva FJ, Pereto J, Moya A (2004) Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev 68:518-537 (Pubitemid 39238281)
40. Gogarten JP, Doolittle WF, Lawrence JG (2002) Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19:2226-2238 (Pubitemid 35440456)
41. Goodfellow M, O'Donnell AG (1993) Handbook of new bacterial systematics. Academic Press, London
42. Goodfellow M, Manfio GP, Chun J (1997) Towards a practical species concept for cultivable bacteria. In: Claridge MD, Dawah HA, Wilson MR (eds) Species: the units of diversity. Chapman and Hall, London, pp 25-59
43. Goodfellow M, Kämpfer P, Busse HJ, Trujillo M, Suzuki K-I, Ludwig W, Whitman WB (2011). Bergey's Manual of Systematic Bacteriology, 2nd Edn, Vol 5, The Actinobacteria, Springer, New York (in press)
44. Gupta RS (2001) The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins. Int Microbiol 4:187-202 (Pubitemid 33771681)
45. Gupta RS, Griffiths E (2002) Critical issues in bacterial phylogeny. Theor Popul Biol 61:423-434 (Pubitemid 38051046)
46. Gupta RS, Pereira M, Chandrasekera C, Johari V (2003) Molecular signatures in protein sequences that are characteristic of cyanobacteria and plastid homologues. Int J Syst Evol Microbiol 53:1833-1842 (Pubitemid 37483840)
47. Harrington CS, On SL (1999) Extensive 16S rRNA gene sequence diversity in Campylobacter hyointestinalis strains: taxonomic and applied implications. Int J Syst Bacteriol 49:1171-1175 (Pubitemid 29320769)
48. Hittinger CT, Carroll SB (2007) Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449:677-681 (Pubitemid 47552089)
49. Hong SH, Kim TY, Lee SY (2004) Phylogenetic analysis based on genome-scale metabolic pathway reaction content. Appl Microbiol Biotechnol 65:203-210 (Pubitemid 39062483)
50. Hooper SD, Berg OG (2003) On the nature of gene innovation: duplication patterns in microbial genomes. Mol Biol Evol 20:945-954 (Pubitemid 36578721)
51. House CH, Fitz-Gibbon ST (2002) Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J Mol Evol 54:539-547 (Pubitemid 34271134)
52. Huang J, Gogarten JP (2006) Ancient horizontal gene transfer can benefit phylogenetic reconstruction. Trends Genet 22:361-366 (Pubitemid 44015971)
53. Hugenholtz P, Goebel BM, Pace NR (1998) Impact of cultureindependent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765-4774 (Pubitemid 28429361)
54. Hull DL (1997) The ideal species concept-and why we can't get it. In: Claridge MF, Dawah HA, Wilson MR (eds) Species: the units of biodiversity. Chapman and Hall, London, pp 357-380
55. Huson DH, Steel M (2004) Phylogenetic trees based on gene content. Bioinformatics 20:2044-2049 (Pubitemid 39236556)
56. Huynen MA, Bork P (1998) Measuring genome evolution. Proc Natl Acad Sci USA 95:5849-5856 (Pubitemid 28248930)
57. Innan H, Kondrashov F (2010) The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet 11:97-108
58. Jeffroy O, Brinkmann H, Delsuc F, Philippe H (2006) Phylogenomics: the beginning of incongruence? Trends Genet 22:225-231
59. Jordan IK, Makarova KS, Spouge JL, Wolf YI, Koonin EV (2001) Lineage-specific gene expansions in bacterial and archaeal genomes. Genome Res 11:555-565 (Pubitemid 32331553)
60. Klenk HP, Goker M (2010) En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 33:175-182
61. Koeppel A, Perry EB, Sikorski J, Krizanc D, Warner A, Ward DM, Rooney AP et al (2008) Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proc Natl Acad Sci USA 105:2504-2509 (Pubitemid 351520543)
62. Kolsto AB (1997) Dynamic bacterial genome organization. Mol Microbiol 24:241-248
63. Konstantinidis KT, Tiedje JM (2005) Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187:6258-6264 (Pubitemid 41318383)
64. Koonin EV (2003) Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol 1:127-136
65. Korbel JO, Snel B, Huynen MA, Bork P (2002) SHOT: a web server for the construction of genome phylogenies. Trends Genet 18:158-162 (Pubitemid 34164642)
66. Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (2010) Bergey's Manual of Systematic Bacteriology, 2nd Edition, Volume 4, The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gennatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae and Planctomycetes, Springer, USA
67. Kunin V, Ouzounis CA (2003) The balance of driving forces during genome evolution in prokaryotes. Genome Res 13:1589-1594 (Pubitemid 36874475)
68. Kunin V, Ahren D, Goldovsky L, Janssen P, Ouzounis CA (2005) Measuring genome conservation across taxa: divided strains and united kingdoms. Nucleic Acids Res 33:616-621 (Pubitemid 40360991)
69. Kunisawa T (1995) Identification and chromosomal distribution of DNA sequence segments conserved since divergence of Escherichia coli and Bacillus subtilis. J Mol Evol 40:585-593
70. Lawrence JG, Retchless AC (2009) The interplay of homologous recombination and horizontal gene transfer in bacterial speciation. Methods Mol Biol 532:29-53
71. Lawrence JG, Retchless AC (2010) The myth of bacterial species and speciation. Biol Philos 25:569-588
72. Lin J, Gerstein M (2000) Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res 10:808-818 (Pubitemid 30433354)
73. Liu B, Knirel YA, Feng L, Perepelov AV, Senchenkova SN, Wang Q, Reeves PR, Wang L (2008) Structure and genetics of Shigella O antigens. FEMS Microbiol Rev 32:627-653 (Pubitemid 351799688)
74. Lopez P, Bapteste E (2009) Molecular phylogeny: reconstructing the forest. C R Biol 332:171-182
75. Lucker S, Wagner M, Maixner F, Pelletier E, Koch H, Vacherie B, Rattei T, Damste JS, Spieck E, Le Paslier D, Daims H (2010) A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc Natl Acad Sci USA 107:13479-13484
76. Ludwig W, Schleifer KH (1994) Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. FEMS Microbiol Rev 15:155-173 (Pubitemid 24323955)
77. Ma HW, Zeng AP (2004) Phylogenetic comparison of metabolic capacities of organisms at genome level. Mol Phylogenet Evol 31:204-213
78. Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S et al (2011) Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 9:467-477
79. Mayden RL (1997) A hierarchy of species concepts: the denouement in the saga of the species problem. In: Claridge MF, Dawah HA, Wilson MR (eds) Species: the units of biodiversity. Chapman and Hall, London, pp 381-382
80. Mayr E (1970) Populations, species and evolution. Harvard University Press, Cambridge
81. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R (2005) The microbial pan-genome. Curr Opin Genet Dev 15:589-594 (Pubitemid 41532330)
82. Meglitsch PA (1954) On the nature of species. Syst Zool 3:491-503
83. Metzker ML (2010) Sequencing technologies: the next generation. Nat Rev Genet 11:31-46
84. Mira A, Klasson L, Andersson SG (2002) Microbial genome evolution: sources of variability. Curr Opin Microbiol 5:506-512
85. Mira A, Martin-Cuadrado AB, D'Auria G, Rodriguez-Valera F (2010) The bacterial pan-genome: a new paradigm in microbiology. Int Microbiol 13:45-57
86. Mocali S, Benedetti A (2010) Exploring research frontiers in microbiology: the challenge of metagenomics in soil microbiology. Res Microbiol 161:497-505
87. Monot M, Honore N, Garnier T, Zidane N, Sherafi D, Paniz- Mondolfi A, Matsuoka M et al (2009) Comparative genomic and phylogeographic analysis of Mycobacterium leprae. Nat Genet 41:1282-1289
88. Moran NA (2003) Tracing the evolution of gene loss in obligate bacterial symbionts. Curr Opin Microbiol 6:512-518 (Pubitemid 37345418)
89. Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner DM, Feldkamp M et al (2010) Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat Genet 42:1140-1143
90. Morschhauser J, Kohler G, Ziebuhr W, Blum-Oehler G, Dobrindt U, Hacker J (2000) Evolution of microbial pathogens. Philos Trans R Soc Lond B Biol Sci 355:695-704 (Pubitemid 30354754)
91. Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304 (Pubitemid 30337055)
92. Okura M, Osawa R, Tokunaga A, Morita M, Arakawa E, Watanabe H (2008) Genetic analyses of the putative O and K antigen gene clusters of pandemic Vibrio parahaemolyticus. Microbiol Immunol 52:251-264
93. O'Malley MA (2007) The nineteenth century roots of 'everything is everywhere'. Nat Rev Microbiol 5:647-651 (Pubitemid 47078772)
94. Pace NR (2009) Mapping the tree of life: progress and prospects. Microbiol Mol Biol Rev 73(4):565-576
95. Pearson T, Okinaka RT, Foster JT, Keim P (2009) Phylogenetic understanding of clonal populations in an era of whole genome sequencing. Infect Genet Evol 9:1010-1019
96. Pei AY, Oberdorf WE, Nossa CW, Agarwal A, Chokshi P, Gerz EA, Jin Z, Lee P et al (2010) Diversity of 16S rRNA genes within individual prokaryotic genomes. Appl Environ Microbiol 76:3886-3897
97. Pena A, Teeling H, Huerta-Cepas J, Santos F, Yarza P, Brito- Echeverria J, Lucio M et al (2010) Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains. ISME J 4:882-895
98. Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J (2009) Metagenomic pyrosequencing and microbial identification. Clin Chem 55:856-866
99. Philippe H, Douady CJ (2003) Horizontal gene transfer and phylogenetics. Curr Opin Microbiol 6:498-505 (Pubitemid 37345416)
100. Planet PJ, Sarkar IN (2005) mILD: a tool for constructing and analyzing matrices of pairwise phylogenetic character incongruence tests. Bioinformatics 21:4423-4424 (Pubitemid 41782937)
101. Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T (2011) Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res 21:599-609
102. Poptsova M (2009) Testing phylogenetic methods to identify horizontal gene transfer. Methods Mol Biol 532:227-240
103. Priest FG, Williams ST (1993) Computer-assisted identification. In: Goodfellow M, O'Donnell AG (eds) Handbook of bacterial systematics. Academic Press, London, pp 362-381
104. Rannala B, Yang Z (2008) Phylogenetic inference using whole genomes. Annu Rev Genomics Hum Genet 9:217-231
105. Rocha EP (2004) Order and disorder in bacterial genomes. Curr Opin Microbiol 7:519-527 (Pubitemid 39297133)
106. Rosenberg MS, Kumar S (2003) Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Mol Biol Evol 20:610-621 (Pubitemid 36437911)
107. Rosselló-Mora R (2003) Opinion: the species problem, can we achieve a universal concept? Syst Appl Microbiol 26:323-326 (Pubitemid 37139753)
108. Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39-67 (Pubitemid 32057196)
109. Schleifer KH (2009) Classification of Bacteria and Archaea: past, present and future. Syst Appl Microbiol 32:533-542
110. Schleifer KH, Stackebrandt E (1983) Molecular systematics of prokaryotes. Annu Rev Microbiol 37:143-187
111. Schouls LM, Schot CS, Jacobs JA (2003) Horizontal transfer of segments of the 16S rRNA genes between species of the Streptococcus anginosus group. J Bacteriol 185:7241-7246 (Pubitemid 37509841)
112. Simpson GG (1961) Principles of animal taxonomy, Columbia University Press, New York
113. Sneath PHA (1992) International code of nomenclature of bacteria (bacteriological code 1990 revision). American Society of Microbiology, Washington
114. Snel B, Bork P, Huynen MA (1999) Genome phylogeny based on gene content. Nat Genet 21:108-110 (Pubitemid 29036294)
115. Snel B, Huynen MA, Dutilh BE (2005) Genome trees and the nature of genome evolution. Annu Rev Microbiol 59:191-209 (Pubitemid 41507429)
116. Soria-Carrasco V, Castresana J (2008) Estimation of phylogenetic inconsistencies in the three domains of life. Mol Biol Evol 25:2319-2329
117. 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 44:846-849 (Pubitemid 24315169)
118. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P, Maiden MC et al (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043-1047 (Pubitemid 34591239)
119. Staley J (2009) The phylogenomic species concept. Microbiology Today, May 09:80-83
120. Sun Y, Wang M, Liu H, Wang J, He X, Zeng J, Guo X, Li K, Cao B, Wang L (2011) Development of an O-antigen serotyping scheme for Cronobacter sakazakii. Appl Environ Microbiol 77:2209-2214
121. Sutcliffe IC (2010) A phylum level perspective on bacterial cell envelope architecture. Trends Microbiol 18:464-470
122. Suyama M, Bork P (2001) Evolution of prokaryotic gene order: genome rearrangements in closely related species. Trends Genet 17:10-13 (Pubitemid 32332968)
123. Switt AI, Soyer Y, Warnick LD, Wiedmann M (2009) Emergence, distribution, and molecular and phenotypic characteristics of Salmonella enterica serotype 4, 5, 12:i:-. Foodborne Pathog Dis 6:407-415
124. Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278:631-637 (Pubitemid 27464953)
125. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV et al (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci USA 102:13950-13955 (Pubitemid 41377684)
126. Tindall BJ, Rosselló-Mora R, Busse HJ, Ludwig W, Kämpfer P (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249-266
127. Ueda K, Seki T, Kudo T, Yoshida T, Kataoka M (1999) Two distinct mechanisms cause heterogeneity of 16S rRNA. J Bacteriol 181:78-82 (Pubitemid 29013656)
128. 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 (Pubitemid 26170913)
129. Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF, van Sinderen D (2007) Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev 71:495-548 (Pubitemid 47429283)
130. Vos M (2011) A species concept for bacteria based on adaptive divergence. Trends Microbiol 19(1):1-7
131. Wang Q, Torzewska A, Ruan X, Wang X, Rozalski A, Shao Z, Guo X, Zhou H, Feng L, Wang L (2010) Molecular and genetic analyses of the putative Proteus O antigen gene locus. Appl Environ Microbiol 76:5471-5478
132. Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088-5090 (Pubitemid 8241042)
133. Wolf YI, Brenner SE, Bash PA, Koonin EV (1999) Distribution of protein folds in the three superkingdoms of life. Genome Res 9:17-26 (Pubitemid 29095145)
134. Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV (2001) Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol 1:8
135. Wolf YI, Rogozin IB, Grishin NV, Koonin EV (2002) Genome trees and the tree of life. Trends Genet 18:472-479
136. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ et al (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462:1056-1060
137. Zhao W, Zhong Y, Yuan H, Wang J, Zheng H, Wang Y, Cen X, Xu F, Bai J, Han X et al (2010) Complete genome sequence of the rifamycin SV-producing Amycolatopsis mediterranei U32 revealed its genetic characteristics in phylogeny and metabolism. Cell Res 20:1096-1108
138. Zuckerkandl E, Pauling L (1965) Molecules as documents of evolutionary history. J Theoret Biol 8:357-366