Archives of Microbiology

, Volume 197, Issue 3, pp 359–370 | Cite as

Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

  • Cristiane C. Thompson
  • Gilda R. Amaral
  • Mariana Campeão
  • Robert A. Edwards
  • Martin F. Polz
  • Bas E. Dutilh
  • David W. Ussery
  • Tomoo Sawabe
  • Jean Swings
  • Fabiano L. Thompson
Opinion Paper

Abstract

Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. Its cornerstone, the prokaryote species has been re-evaluated twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. Ultimately, we will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.

Keywords

Bacteria Archaea Microbes Taxonomy Genomics Evolution Open access 

References

  1. Achtman M, Wagner M (2008) Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 6:431–440. doi:10.1038/nrmicro1872 PubMedGoogle Scholar
  2. Alvarez-Pérez S, de Vega C, Herrera CM (2013) Multilocus sequence analysis of nectar pseudomonads reveals high genetic diversity and contrasting recombination patterns. PLoS One 8:e75797. doi:10.1371/journal.pone.0075797 CrossRefPubMedCentralPubMedGoogle Scholar
  3. Amaral GRS, Dias GM, Wellington-Oguri M et al (2014) Genotype to phenotype: identification of diagnostic vibrio phenotypes using whole genome sequences. Int J Syst Evol Microbiol 64:357–365. doi:10.1099/ijs.0.057927-0 CrossRefPubMedGoogle Scholar
  4. Auch AF, von Jan M, Klenk H-P, Göker M (2010) Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134. doi:10.4056/sigs.531120 CrossRefPubMedCentralPubMedGoogle Scholar
  5. Aziz RK, Bartels D, Best AA et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. doi:10.1186/1471-2164-9-75 CrossRefPubMedCentralPubMedGoogle Scholar
  6. Bayjanov JR, Molenaar D, Tzeneva V et al (2012) PhenoLink—a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains. BMC Genomics 13:170. doi:10.1186/1471-2164-13-170 CrossRefPubMedCentralPubMedGoogle Scholar
  7. Brown JR, Douady CJ, Italia MJ et al (2001) Universal trees based on large combined protein sequence data sets. Nat Genet 28:281–285. doi:10.1038/90129 CrossRefPubMedGoogle Scholar
  8. Brown MV, Lauro FM, DeMaere MZ et al (2012) Global biogeography of SAR11 marine bacteria. Mol Syst Biol 8:595. doi:10.1038/msb.2012.28 CrossRefPubMedCentralPubMedGoogle Scholar
  9. Cadillo-Quiroz H, Didelot X, Held NL et al (2012) Patterns of gene flow define species of thermophilic Archaea. PLoS Biol 10:e1001265. doi:10.1371/journal.pbio.1001265 CrossRefPubMedCentralPubMedGoogle Scholar
  10. Caro-Quintero A, Konstantinidis KT (2012) Bacterial species may exist, metagenomics reveal. Environ Microbiol 14:347–355. doi:10.1111/j.1462-2920.2011.02668.x CrossRefPubMedGoogle Scholar
  11. Chun J, Rainey FA (2014) Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 64:316–324. doi:10.1099/ijs.0.054171-0 CrossRefPubMedGoogle Scholar
  12. 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. doi:10.1099/mic.0.26515-0 CrossRefPubMedGoogle Scholar
  13. Coenye T, Gevers D, Van de Peer Y et al (2005) Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev 29:147–167PubMedGoogle Scholar
  14. Cohan F (2001) Bacterial species and speciation. Syst Biol 50:513–524CrossRefPubMedGoogle Scholar
  15. Colwell RR (1970) Polyphasic taxonomy of the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. J Bacteriol 104:410–433PubMedCentralPubMedGoogle Scholar
  16. Cordero OX, Polz MF (2014) Explaining microbial genomic diversity in light of evolutionary ecology. Nat Rev Microbiol 12:263–273. doi:10.1038/nrmicro3218 CrossRefPubMedGoogle Scholar
  17. Cordero OX, Ventouras LA, DeLong EF, Polz MF (2012) Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations. Proc Natl Acad Sci USA 109:20059–20064. doi:10.1073/pnas.1213344109 CrossRefPubMedCentralPubMedGoogle Scholar
  18. Cuevas DA, Garza D, Sanchez SE et al (2014) Elucidating genomic gaps using phenotypic profiles [v1; ref status: approved with reservations 1, http://f1000r.es/488]. F1000Research 3:210. doi:10.12688/f1000research.5140.1
  19. De Ley J (1970) Reexamination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleic acid. J Bacteriol 101:738–754PubMedCentralPubMedGoogle Scholar
  20. De Queiroz K (2005) Ernst Mayr and the modern concept of species. Proc Natl Acad Sci USA 102(Suppl1):6600–6607. doi:10.1073/pnas.0502030102 CrossRefPubMedCentralPubMedGoogle Scholar
  21. Denef VJ, Mueller RS, Banfield JF (2010) AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME J 4:599–610. doi:10.1038/ismej.2009.158 CrossRefPubMedGoogle Scholar
  22. Didelot X, Bowden R, Wilson DJ et al (2012) Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 13:601–612. doi:10.1038/nrg3226 CrossRefPubMedGoogle Scholar
  23. Doi Y, Hazen TH, Boitano M, et al (2014) Whole genome assembly of Klebsiella pneumoniae co-producing NDM-1 and OXA-232 carbapenemases using single-molecule, real-time sequencing. Antimicrob Agents Chemother 58(10):5947–5953. doi:10.1128/AAC.03180-14 CrossRefPubMedGoogle Scholar
  24. Doolittle WF, Papke RT (2006) Genomics and the bacterial species problem. Genome Biol 7:116. doi:10.1186/gb-2006-7-9-116 CrossRefPubMedCentralPubMedGoogle Scholar
  25. Doolittle WF, Zhaxybayeva O (2009) On the origin of prokaryotic species. Genome Res 19:744–756. doi:10.1101/gr.086645.108 CrossRefPubMedGoogle Scholar
  26. Dutilh BE, Backus L, Edwards RA et al (2013) Explaining microbial phenotypes on a genomic scale: GWAS for microbes. Brief Funct Genomics 12:366–380. doi:10.1093/bfgp/elt008 CrossRefPubMedCentralPubMedGoogle Scholar
  27. Dutilh BE, Thompson CC, Vicente AC et al (2014) Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions. BMC Genomics 15:654. doi:10.1186/1471-2164-15-654 CrossRefPubMedCentralPubMedGoogle Scholar
  28. Dykhuizen D (2005) Species numbers in bacteria. Proc Calif Acad Sci 56:62–71PubMedCentralPubMedGoogle Scholar
  29. Ellegaard KM, Klasson L, Näslund K et al (2013) Comparative genomics of Wolbachia and the bacterial species concept. PLoS Genet 9:e1003381. doi:10.1371/journal.pgen.1003381 CrossRefPubMedCentralPubMedGoogle Scholar
  30. Forde BM, Ben Zakour NL, Stanton-Cook M et al (2014) The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone. PLoS One 9:e104400. doi:10.1371/journal.pone.0104400 CrossRefPubMedCentralPubMedGoogle Scholar
  31. Franzosa EA, Morgan XC, Segata N et al (2014) Relating the metatranscriptome and metagenome of the human gut. Proc Natl Acad Sci USA. doi:10.1073/pnas.1319284111 PubMedCentralPubMedGoogle Scholar
  32. Fraser C, Hanage WP, Spratt BG (2007) Recombination and the nature of bacterial speciation. Science 315:476–480. doi:10.1126/science.1127573.Recombination CrossRefPubMedCentralPubMedGoogle Scholar
  33. Fraser C, Alm EJ, Polz MF et al (2009) The bacterial species challenge: ecological diversity. Science 323:741–746CrossRefPubMedGoogle Scholar
  34. Gevers D, Cohan FM, Lawrence JG et al (2005) Re-evaluating prokaryotic species. Nat Rev Microbiol 3:733–739CrossRefPubMedGoogle Scholar
  35. Giovannoni SJ, Tripp HJ, Givan S et al (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309:1242–1245. doi:10.1126/science.1114057 CrossRefPubMedGoogle Scholar
  36. Haley BJ, Grim CJ, Hasan NA et al (2010) Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae. BMC Microbiol 10:154. doi:10.1186/1471-2180-10-154 CrossRefPubMedCentralPubMedGoogle Scholar
  37. Hanage WP (2013) Fuzzy species revisited. BMC Biol 11:41. doi:10.1186/1741-7007-11-41 CrossRefPubMedCentralPubMedGoogle Scholar
  38. Hanage WP, Fraser C, Spratt BG (2005) Fuzzy species among recombinogenic bacteria. BMC Biol 3:6. doi:10.1186/1741-7007-3-6 CrossRefPubMedCentralPubMedGoogle Scholar
  39. Huang K, Brady A, Mahurkar A et al (2014) MetaRef: a pan-genomic database for comparative and community microbial genomics. Nucleic Acids Res 42:D617–D624. doi:10.1093/nar/gkt1078 CrossRefPubMedCentralPubMedGoogle Scholar
  40. Hunt DE, David LA, Gevers D et al (2008) Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science 320:1081–1085. doi:10.1126/science.1157890 CrossRefPubMedGoogle Scholar
  41. Kämpfer P, Glaeser SP (2012) Prokaryotic taxonomy in the sequencing era—the polyphasic approach revisited. Environ Microbiol 14:291–317. doi:10.1111/j.1462-2920.2011.02615.x CrossRefPubMedGoogle Scholar
  42. Karlin S, Burge C (1995) Dinucleotide relative abundance extremes: a genomic signature. Trends Genet 11:283–290CrossRefPubMedGoogle Scholar
  43. Karp PD, Ouzounis CA, Moore-Kochlacs C et al (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 33:6083–6089. doi:10.1093/nar/gki892 CrossRefPubMedCentralPubMedGoogle Scholar
  44. Kashtan N, Roggensack SE, Rodrigue S et al (2014) Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344:416–420. doi:10.1126/science.1248575 CrossRefPubMedGoogle Scholar
  45. Klenk H-P, Göker M (2010) En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 33:175–182. doi:10.1016/j.syapm.2010.03.003 CrossRefPubMedGoogle Scholar
  46. Konstantinidis KT, DeLong EF (2008) Genomic patterns of recombination, clonal divergence and environment in marine microbial populations. ISME J 2:1052–1065. doi:10.1038/ismej.2008.62 CrossRefPubMedGoogle Scholar
  47. Konstantinidis KT, Stackebrandt E (2013) Defining taxonomic ranks. In: Rosenberg E, DeLong EF, Lory S, et al (eds) Prokaryotes (4th ed). Prokaryotic Biol. Symbiotic Assoc., 4th edn p 229Google Scholar
  48. Konstantinidis KT, Tiedje JM (2005) Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187:6258–6264. doi:10.1128/JB.187.18.6258 CrossRefPubMedCentralPubMedGoogle Scholar
  49. Kyrpides NC (1999) Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide. Bioinformatics 15:773–774CrossRefPubMedGoogle Scholar
  50. Lan R, Reeves PR (2000) Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol 8:396–401CrossRefPubMedGoogle Scholar
  51. Larsen MV, Cosentino S, Lukjancenko O et al (2014) Benchmarking of methods for genomic taxonomy. J Clin Microbiol 52:1529–1539. doi:10.1128/JCM.02981-13 CrossRefPubMedCentralPubMedGoogle Scholar
  52. Li J, Jia H, Cai X et al (2014) An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol. doi:10.1038/nbt.2942 Google Scholar
  53. Mallet J (2008) Hybridization, ecological races and the nature of species: empirical evidence for the ease of speciation. Philos Trans R Soc Lond B Biol Sci 363:2971–2986. doi:10.1098/rstb.2008.0081 CrossRefPubMedCentralPubMedGoogle Scholar
  54. Markowitz VM, Korzeniewski F, Palaniappan K et al (2006) The integrated microbial genomes (IMG) system. Nucleic Acids Res 34:D344–D348. doi:10.1093/nar/gkj024 CrossRefPubMedCentralPubMedGoogle Scholar
  55. Markowitz VM, Chen I-MA, Palaniappan K et al (2014) IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res 42:D560–D567. doi:10.1093/nar/gkt963 CrossRefPubMedCentralPubMedGoogle Scholar
  56. Mayr E (1942) Systematics and the origin of species—from the viewpoint of a zoologist. Harvard Univ. Press, CambridgeGoogle Scholar
  57. Mick E, Sorek R (2014) High-resolution metagenomics. Nat Biotechnol 32:750–751. doi:10.1038/nbt.2962 CrossRefPubMedGoogle Scholar
  58. Moreira APB, Duytschaever G, Tonon LAC et al (2014a) Photobacterium sanctipauli sp. nov. isolated from bleached Madracis decactis (Scleractinia) in the St Peter & St Paul Archipelago, Mid-Atlantic Ridge, Brazil. Peer J 2:e427. doi:10.7717/peerj.427 CrossRefPubMedCentralPubMedGoogle Scholar
  59. Moreira APB, Duytschaever G, Tonon LAC et al (2014b) Vibrio madracius sp. nov. isolated from Madracis decactis (Scleractinia) in St Peter & St Paul Archipelago, Mid-Atlantic Ridge, Brazil. Curr Microbiol 2:e427. doi:10.1007/s00284-014-0600-1 Google Scholar
  60. Nesbø CL, Dlutek M, Doolittle WF (2006) Recombination in Thermotoga: implications for species concepts and biogeography. Genetics 172:759–769. doi:10.1534/genetics.105.049312 CrossRefPubMedCentralPubMedGoogle Scholar
  61. Nielsen HB, Almeida M, Juncker AS et al (2014) Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol. doi:10.1038/nbt.2939 Google Scholar
  62. Overbeek R, Olson R, Pusch GD et al (2014) The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42:D206–D214. doi:10.1093/nar/gkt1226 CrossRefPubMedCentralPubMedGoogle Scholar
  63. Pagani I, Liolios K, Jansson J et al (2012) The Genomes OnLine Database (GOLD) v. 4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 40:D571–D579. doi:10.1093/nar/gkr1100 CrossRefPubMedCentralPubMedGoogle Scholar
  64. Polz MF, Hunt DE, Preheim SP, Weinreich DM (2006) Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philos Trans R Soc Lond B Biol Sci 361:2009–2021. doi:10.1098/rstb.2006.1928 CrossRefPubMedCentralPubMedGoogle Scholar
  65. Polz MF, Alm EJ, Hanage WP (2013) Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends Genet 29:170–175. doi:10.1016/j.tig.2012.12.006 CrossRefPubMedCentralPubMedGoogle Scholar
  66. Preheim SP, Timberlake S, Polz MF (2011) Merging taxonomy with ecological population prediction in a case study of Vibrionaceae. Appl Environ Microbiol 77:7195–7206. doi:10.1128/AEM.00665-11 CrossRefPubMedCentralPubMedGoogle Scholar
  67. Ramasamy D, Mishra AK, Lagier J-C et al (2014) A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol 64:384–391. doi:10.1099/ijs.0.057091-0 CrossRefPubMedGoogle Scholar
  68. Rinke C, Schwientek P, Sczyrba A et al (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431–437. doi:10.1038/nature12352 CrossRefPubMedGoogle Scholar
  69. Rodriguez-Valera F, Martin-Cuadrado A-B, Rodriguez-Brito B et al (2009) Explaining microbial population genomics through phage predation. Nat Rev Microbiol 7:828–836. doi:10.1038/nrmicro2235 CrossRefPubMedGoogle Scholar
  70. Rohwer F, Edwards R (2002) The phage proteomic tree: a genome-based taxonomy for phage. J Bacteriol 184:4529–4535. doi:10.1128/JB.184.16.4529 CrossRefPubMedCentralPubMedGoogle Scholar
  71. Romero P, Wagg J, Green ML et al (2005) Computational prediction of human metabolic pathways from the complete human genome. Genome Biol 6:R2. doi:10.1186/gb-2004-6-1-r2 CrossRefPubMedCentralPubMedGoogle Scholar
  72. Rosselló-Móra R (2012) Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories. Environ Microbiol 14:318–334. doi:10.1111/j.1462-2920.2011.02599.x CrossRefPubMedGoogle Scholar
  73. Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67CrossRefPubMedGoogle Scholar
  74. Sen A, Daubin V, Abrouk D, Gifford I, Berry AM, Normand P (2014) Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders ‘Frankiales’ and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov. Int J Syst Evol Microbiol 64:3821–3832. doi:10.1099/ijs.0.063966-0
  75. Shapiro BJ, Polz MF (2014) Ordering microbial diversity into ecologically and genetically cohesive units. Trends Microbiol 22:235–247. doi:10.1016/j.tim.2014.02.006 CrossRefPubMedGoogle Scholar
  76. Shapiro BJ, Friedman J, Cordero OX et al (2012) Population genomics of early events in the ecological differentiation of bacteria. Science 336:48–51. doi:10.1126/science.1218198 CrossRefPubMedCentralPubMedGoogle Scholar
  77. Shiwa Y, Yanase H, Hirose Y et al (2014) Complete genome sequence of Enterococcus mundtii QU 25, an efficient l-(+)-Lactic Acid-producing bacterium. DNA Res 21:369–377. doi:10.1093/dnares/dsu003 CrossRefPubMedCentralPubMedGoogle Scholar
  78. Sneath PHA, Sokal RR (1973) The principles and practice of numerical classification. Numer. TaxonGoogle Scholar
  79. Snipen L, Ussery DW (2010) Standard operating procedure for computing pangenome trees. Stand Genomic Sci 2:135–141. doi:10.4056/sigs.38923 CrossRefPubMedCentralPubMedGoogle Scholar
  80. Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155Google Scholar
  81. Stackebrandt E, Frederiksen W, Garrity GM 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. doi:10.1099/ijs.0.02360-0.02360 CrossRefPubMedGoogle Scholar
  82. Stackebrandt E, Smith D, Casaregola S et al (2014) Deposit of microbial strains in public service collections as part of the publication process to underpin good practice in science. Springerplus 3:208. doi:10.1186/2193-1801-3-208 CrossRefPubMedCentralPubMedGoogle Scholar
  83. Staley JT (2006) The bacterial species dilemma and the genomic–phylogenetic species concept. Philos Trans R Soc Lond B Biol Sci 361:1899–1909. doi:10.1098/rstb.2006.1914 CrossRefPubMedCentralPubMedGoogle Scholar
  84. Staley JT (2009) Universal species concept: Pipe dream or a step toward unifying biology? J Ind Microbiol Biotechnol 36:1331–1336. doi:10.1007/s10295-009-0642-8 CrossRefPubMedGoogle Scholar
  85. Tamames J, Rosselló-Móra R (2012) On the fitness of microbial taxonomy. Trends Microbiol 20:514–516. doi:10.1016/j.tim.2012.08.012 CrossRefPubMedGoogle Scholar
  86. Thompson CC, Vicente ACP, Souza RC et al (2009) Genomic taxonomy of vibrios. BMC Evol Biol 9:258. doi:10.1186/1471-2148-9-258 CrossRefPubMedCentralPubMedGoogle Scholar
  87. Thompson C, Vieira NM, Vicente A, Thompson F (2011a) Towards a genome based taxonomy of Mycoplasmas. Infect Genet Evol 11:1798–1804. doi:10.1016/j.meegid.2011.07.020 CrossRefPubMedGoogle Scholar
  88. Thompson FL, Thompson CC, Dias GM et al (2011b) The genus Listonella MacDonell and Colwell 1986 is a later heterotypic synonym of the genus Vibrio Pacini 1854 (Approved Lists 1980)—a taxonomic opinion. Int J Syst Evol Microbiol 61:3023–3027. doi:10.1099/ijs.0.030015-0 CrossRefPubMedCentralPubMedGoogle Scholar
  89. Thompson CC, Chimetto L, Edwards RA et al (2013a) Microbial genomic taxonomy. BMC Genomics 14:913. doi:10.1186/1471-2164-14-913 CrossRefPubMedCentralPubMedGoogle Scholar
  90. Thompson CC, Emmel VE, Fonseca EL et al (2013b) Streptococcal taxonomy based on genome sequence analyses. F1000Res 2:67. doi:10.12688/f1000research.2-67.v1 PubMedCentralPubMedGoogle Scholar
  91. Thompson CC, Silva GZ, Vieira NM et al (2013c) Genomic taxonomy of the genus Prochlorococcus. Microb Ecol 66:752–762. doi:10.1007/s00248-013-0270-8 CrossRefPubMedGoogle Scholar
  92. Tindall BJ, Rosselló-Móra R, Busse H-J et al (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249–266. doi:10.1099/ijs.0.016949-0 CrossRefPubMedGoogle Scholar
  93. Vandamme P, Peeters C (2014) Time to revisit polyphasic taxonomy. Antonie Van Leeuwenhoek 106:57–65CrossRefPubMedGoogle Scholar
  94. Wayne LG, Brenner DJ, Colwell RR, et al (1987) International Committee on Systematic Bacteriology announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Bacteriol 463–464Google Scholar
  95. Whitman WB (2009) The modern concept of the procaryote. J Bacteriol 191:2000–2005. doi:10.1128/JB.00962-08 Discussion 2006–2007CrossRefPubMedCentralPubMedGoogle Scholar
  96. Wiedenbeck J, Cohan FM (2011) Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev 35:957–976. doi:10.1111/j.1574-6976.2011.00292.x CrossRefPubMedGoogle Scholar
  97. Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088–5090CrossRefPubMedCentralPubMedGoogle Scholar
  98. Woyke T, Xie G, Copeland A et al (2009) Assembling the marine metagenome, one cell at a time. PLoS One 4:e5299. doi:10.1371/journal.pone.0005299 CrossRefPubMedCentralPubMedGoogle Scholar
  99. Wright F (1990) The effective number of codons used in a gene. Gene 87:23–29CrossRefPubMedGoogle Scholar
  100. Wu D, Hugenholtz P, Mavromatis K et al (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462:1056–1060. doi:10.1038/nature08656.A CrossRefPubMedCentralPubMedGoogle Scholar
  101. Yarza P, Richter M, Peplies J et al (2008) The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250CrossRefPubMedGoogle Scholar
  102. Zhi X-Y, Zhao W, Li W-J, Zhao G-P (2012) Prokaryotic systematics in the genomics era. Antonie Van Leeuwenhoek 101:21–34. doi:10.1007/s10482-011-9667-x CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Cristiane C. Thompson
    • 1
  • Gilda R. Amaral
    • 1
  • Mariana Campeão
    • 1
  • Robert A. Edwards
    • 1
    • 2
    • 3
  • Martin F. Polz
    • 4
  • Bas E. Dutilh
    • 1
    • 5
  • David W. Ussery
    • 6
  • Tomoo Sawabe
    • 7
  • Jean Swings
    • 1
    • 8
  • Fabiano L. Thompson
    • 1
    • 9
  1. 1.Laboratory of Microbiology, Institute of BiologyFederal University of Rio de Janeiro (UFRJ)Rio de JaneiroBrazil
  2. 2.San Diego State UniversitySan DiegoUSA
  3. 3.Argonne National LaboratoryArgonneUSA
  4. 4.Massachusetts Institute of TechnologyCambridgeUSA
  5. 5.Radbould UniversityNijmegenThe Netherlands
  6. 6.BioSciences DivisionOak Ridge National LabsOak RidgeUSA
  7. 7.Laboratory of Microbiology, Faculty of Fisheries SciencesHokkaido UniversityHakodateJapan
  8. 8.Laboratorium voor MicrobiologieGhent UniversityGhentBelgium
  9. 9.SAGE-COPPE-UFRJRio de JaneiroBrazil

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