Genome sequences as the type material for taxonomic descriptions of prokaryotes

Systematic and Applied Microbiology

Volumn 38, Issue 4, 2015, Pages 217-222

  Whitman, William B ^a  

^a UNIVERSITY OF GEORGIA   (United States)

Author keywords

Bacteriological code; Genomics; Type strain

Indexed keywords

GENOMIC DNA; RNA 16S; BACTERIAL DNA;

BACTERIOLOGY; DNA DNA HYBRIDIZATION; DNA SEQUENCE; ENDOSYMBIONT; GENE SEQUENCE; GENE TRANSFER; GENOME SIZE; GENOMICS; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; PROKARYOTE; REVIEW; SPECIES IDENTIFICATION; TAXONOMIC RANK; TAXONOMY; TYPE STRAIN; BACTERIAL GENOME; BACTERIUM; CLASSIFICATION; GENETICS;

PROKARYOTA;

BACTERIA; DNA, BACTERIAL; GENOME, BACTERIAL; GENOMICS; SEQUENCE ANALYSIS, DNA;

EID: 84929324905     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2015.02.003     Document Type: Review

References (62)

1. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., Sherlock G. Gene ontology: tool for the unification of biology. Nat. Genet. 2000, 25:25-29.
2. Auch A.F., Klenk H.-P., Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand. Genom. Sci. 2010, 2:142.
3. Auch A.F., von Jan M., Klenk H.-P., Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand. Genom. Sci. 2010, 2:117.
4. Battistuzzi F.U., Feijao A., Hedges S.B. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol. Biol. 2004, 4:44.
5. Blainey P.C., Mosier A.C., Potanina A., Francis C.A., Quake S.R. Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PLoS ONE 2011, 6:e16626.
6. Blank C.E. An expansion of age constraints for microbial clades that lack a conventional fossil record using phylogenomic dating. J. Mol. Evol. 2011, 73:188-208.
7. Caccone A., Desalle R., Powell J.R. Calibration of the change in thermal-stability of DNA duplexes and degree of base pair mismatch. J. Mol. Evol. 1988, 27:212-216.
8. Chain P.S., Grafham D.V., Fulton R.S., Fitzgerald M.G., Hostetler J., Muzny D., Ali J., Birren B., Bruce D.C., Buhay C., Cole J.R., Ding Y., Dugan S., Field D., Garrity G.M., Gibbs R., Graves T., Han C.S., Harrison S.H., Highlander S., Hugenholtz P., Khouri H.M., Kodira C.D., Kolker E., Kyrpides N.C., Lang D., Lapidus A., Malfatti S.A., Markowitz V., Metha T., Nelson K.E., Parkhill J., Pitluck S., Qin X., Read T.D., Schmutz J., Sozhamannan S., Sterk P., Strausberg R.L., Sutton G., Thomson N.R., Tiedje J.M., Weinstock G., Wollam A., Detter J.C. Genomics. Genome project standards in a new era of sequencing. Science 2009, 326:236-237.
9. Chun J., Rainey F.A. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int. J. Syst. Evol. Microbiol. 2014, 64:316-324.
10. Colwell R.R. Polyphasic taxonomy of bacteria. Culture collections of Microorganisms 1970, 421-436. University of Tokyo Press, Tokyo. H. Iizuka, T. Hasegawa (Eds.).
11. De La Torre J.R., Walker C.B., Ingalls A.E., Könneke M., Stahl D.A. Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ. Microbiol. 2008, 10:810-818.
12. Gevers D., Cohan F.M., Lawrence J.G., Spratt B.G., Coenye T., Feil E.J., Stackebrandt E., Van de Peer Y., Vandamme P., Thompson F.L., Swings J. Opinion: re-evaluating prokaryotic species. Nat. Rev. Microbiol. 2005, 3:733-739.
13. Goodfellow M. International Committee on Systematic Bacteriology XVIth International Congress of Microbiology: Minutes of the Meetings, 2, 3, and 5 July 1994, Prague, Czech Republic. Int. J. Syst. Bacteriol. 1995, 45:613-615.
14. Goris J., Konstantinidis K.T., Klappenbach J.A., Coenye T., Vandamme P., Tiedje J.M. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 2007, 57:81-91.
15. Greub G. International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of the Chlamydiae: Minutes of the inaugural closed meeting, 21 March 2009, Little Rock, AR, USA. Int. J. Syst. Evol. Microbiol. 2010, 60:2691-2693.
16. Hatzenpichler R., Lebedeva E.V., Spieck E., Stoecker K., Richter A., Daims H., Wagner M. A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:2134-2139.
17. Johnson J.L., Whitman W.B. Similarity analysis of DNAs. Methods for General and Molecular Microbiology 2007, 624-652. ASM Press, Washington, DC. third ed. C.A. Reddy (Ed.).
18. Johnson J.L., Whitman W.B. Similarity analysis of DNAs. Methods for General and Molecular Microbiology 2007, 624-652. ASM Press, Washington, DC. 3rd ed. R. CA. (Ed.).
19. Kampfer P., Glaeser S.P. Prokaryotic taxonomy in the sequencing era - the polyphasic approach revisited. Environ. Microbiol. 2012, 14:291-317.
20. Kim M., Park S.C., Baek I., Chun.J. Large-scale evaluation of experimentally determined DNA G+C contents with whole genome sequences of prokaryotes. Syst. Appl. Microbiol. 2014, 37:95-99.
21. Klenk H.-P., Göker M. En route to a genome-based classification of Archaea and Bacteria?. Syst. Appl. Microbiol. 2010, 33:175-182.
22. Konneke M., Bernhard A.E., de la Torre J.R., Walker C.B., Waterbury J.B., Stahl D.A. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 2005, 437:543-546.
23. Konstantinidis K.T., Tiedje J.M. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:2567-2572.
24. Krypides N.C., Woyke T., Eisen J.A., Garrity G., Lilburn T.G., Beck B., Whitman W.B., Hugenholtz P., Klenk H.P. Genomic encyclopedia of type strains. Phase I: the one thousand microbial genomes (KMG-I) project. Stand. Genom. Sci. 2014, 9:1278-1284.
25. Kuo C.H., Ochman H. Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria. Biol. Dir. 2009, 4:35.
26. Kyrpides N.C., Hugenholtz P., Eisen J.A., Woyke T., Goker M., Parker C.T., Amann R., Beck B.J., Chain P.S.G., Chun J., Colwell R.R., Danchin A., Dawyndt P., Dedeurwaerdere T., DeLong E.F., Detter J.C., De Vos P., Donohue T.J., Dong X.-Z., Ehrlich D.S., Fraser C., Gibbs R., Gilbert J., Gilna P., Glockner F.O., Jansson J.K., Keasling J.D., Knight R., Labeda D., Lapidus A., Lee J.-S., Li W.-J., Ma J., Markowitz V., Moore E.R.B., Morrison M., Meyer F., Nelson K.E., Ohkuma M., Ouzounis C.A., Pace N., Parkhill J., Qin N., Rossello-Mora R., Sikorski J., Smith D., Sogin M., Stevens R., Stingl U., Suzuki K.-I., Taylor D., Tiedje J.M., Tindall B., Wagner M., Weinstock G., Weissenbach J., White O., Wang J., Zhang L., Zhou Y.-G., Field D., Whitman W.B., Garrity G.M., Klenk H.-P. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol. 2014, 12:e1001920.
27. Labeda D. International Committee on Systematic Bacteriology: IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Int. J. Syst. Evol. Microbiol. 2000, 50:2245-2247.
28. Lapage S.P., Sneath P.H.A., Lessel E.F., Skerman V.B.D., Seeliger H.P.R., Clark W.A. International Code of Nomenclature of Bacteria 1992, American Society for Microbiology, Washington, DC.
29. Lasher C., Dyszynski G., Everett K., Edmonds J., Ye W., Sheldon W., Wang S., Joye S.B., Moran M.A., Whitman W.B. The diverse bacterial community in intertidal, anaerobic sediments at Sapelo Island, Georgia. Microb. Ecol. 2009, 58:244-261.
30. Lebedeva E.V., Hatzenpichler R., Pelletier E., Schuster N., Hauzmayer S., Bulaev A., Grigor'eva N.V., Galushko A., Schmid M., Palatinszky M., Le Paslier D., Daims H., Wagner M. Enrichment and Genome Sequence of the Group I.1a Ammonia-Oxidizing Archaeon "Ca Nitrosotenuis uzonensis" Representing a Clade Globally Distributed in Thermal Habitats. PLoS ONE 2013, 8:e80835.
31. Lehtovirta-Morley L.E., Stoecker K., Vilcinskas A., Prosser J.I., Nicol G.W. Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:15892-15897.
32. Li X., Huang Y., Whitman W.B. The relationship of the whole genome sequence identity to DNA hybridization varies between genera of prokaryotes. Antonie van Leeuenhoek 2014, 106. xxx-xxx.
33. Ludwig W., Euzeby J., Schumann P., Busse H.J., Trujillo M.E., Kaempfer P., Whitman W.B. Road map of the Actinobacteria. Bergey's Manual of Systematic Bacteriology 2012, vol. 5:1-28. Springer, New York, NY. second ed.
34. Meier-Kolthoff J.P., Auch A.F., Klenk H.P., Goker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform. 2013, 14:60.
35. Meier-Kolthoff J.P., Klenk H.P., Goker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int. J. Syst. Evol. Microbiol. 2014, 64:352-356.
36. Mende D.R., Sunagawa S., Zeller G., Bork P. Accurate and universal delineation of prokaryotic species. Nat. Methods 2013, 10:881-884.
37. Metchnikoff E. Pasteuria ramosa, un representant des bacteries a division longitudinale. Ann. Inst. Pasteur (Paris) 1888, 2:165-170.
38. Moore E.R., Mihaylova S.A., Vandamme P., Krichevsky M.I., Dijkshoorn L. Microbial systematics and taxonomy: relevance for a microbial commons. Res. Microbiol. 2010, 161:430-438.
39. Mosier A.C., Allen E.E., Kim M., Ferriera S., Francis C.A. Genome Sequence of "Candidatus Nitrosopumilus salaria" BD31, an Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary. J. Bacteriol. 2012, 194:2121-2122.
40. Murray R.G.E. Taxonomic note: a rule about the deposition of type strains. Int. J. Syst. Bacteriol. 1996, 46:831.
41. Murray R.G.E., Schleifer K.H. Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes. Int. J. Syst. Bacteriol. 1994, 44:174-176.
42. Murray R.G.E., Stackebrandt E. Taxonomic note: implementation of the provisional status candidatus for incompletely described procaryotes. Int. J. Syst. Bacteriol. 1995, 45:186-187.
43. Park S.-J., Kim J.-G., Jung M.-Y., Kim S.-J., Cha I.-T., Ghai R., Martín-Cuadrado A.-B., Rodríguez-Valera F., Rhee.S.-K. Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus sediminis" AR2, from Svalbard in the Arctic Circle. J. Bacteriol. 2012, 194:6948-6949.
44. Park S.-J., Kim J.-G., Jung M.-Y., Kim S.-J., Cha I.-T., Kwon K., Lee J.-H., Rhee S.-K. Draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus koreensis" AR1, from Marine Sediment. J. Bacteriol. 2012, 194:6940-6941.
45. Ramasamy D., Mishra A.K., Lagier J.C., Padhmanabhan R., Rossi M., Sentausa E., Raoult D., Fournier P.E. A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int. J. Syst. Evol. Microbiol. 2014, 64:384-391.
46. Richter M., Rosselló-Móra.R. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:19126-19131.
47. Rosselló-Móra R. DNA-DNA reassociation methods applied to microbial taxonomy and their critical evaluation. Molecular Identification, Systematics, and Population Structure of Prokaryotes 2006, 23-50. Springer-Verlag, Berlin. E. Stackebrandt (Ed.).
48. Rossello-Mora R., Amann R. Past and future species descriptions for Bacteria and Archaea. Syst. Appl. Microbiol. 2015, 38:209-216.
49. Rossello-Mora R., Amann R. The species concept for prokaryotes. FEMS Microbiol. Rev. 2001, 25:39-67.
50. Schleifer K.H. Classification of Bacteria and Archaea: past, present and future. Syst. Appl. Microbiol. 2009, 32:533-542.
51. Skerman V.B.D., McGowan V., Sneath P.H.A. Approved Lists of Bacterial Names 1989, American Society for Microbiology, Washington, DC.
52. Sneath P.H.A., Brenner D.J. Official" nomenclature lists. ASM News 1992, 58:175.
53. Stieglmeier M., Klingl A., Alves R.J.E., Rittmann S.K.-M.R., Melcher M., Leisch N., Schleper C. Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota. Int. J. Syst. Evol. Microbiol. 2014, 64:2738-2752.
54. Sutcliffe I.C., Trujillo M.E., Goodfellow M. A call to arms for systematists: revitalising the purpose and practises underpinning the description of novel microbial taxa. Antonie Van Leeuwenhoek 2012, 101:13-20.
55. Thomas V., Casson N., Greub G. Criblamydia sequanensis, a new intracellular Chlamydiales isolated from Seine river water using amoebal co-culture. Environ. Microbiol. 2006, 8:2125-2135.
56. Tindall B.J., Rossello-Mora R., Busse H.J., Ludwig W., Kampfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int. J. Syst. Evol. Microbiol. 2010, 60:249-266.
57. Vandamme P., Peeters C. Time to revisit polyphasic taxonomy. Antonie Van Leeuwenhoek 2014, 106:57-65.
58. Vandamme P., Pot B., Gillis M., de Vos P., Kersters K., Swings J. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 1996, 60:407-438.
59. Wayne L., Brenner D., Colwell R., Grimont P., Kandler O., Krichevsky M., Moore L., Moore W., Murray R., Stackebrandt E. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 1987, 37:463-464.
60. Whitman W.B. Intent of the nomenclatural Code and recommendations about naming new species based on genomic sequences. Bull. BISMiS 2011, 2:135-140.
61. Wu D., Hugenholtz P., Mavromatis K., Pukall R., Dalin E., Ivanova N.N., Kunin V., Goodwin L., Wu M., Tindall B.J., Hooper S.D., Pati A., Lykidis A., Spring S., Anderson I.J., D'Haeseleer P., Zemla A., Singer M., Lapidus A., Nolan M., Copeland A., Han C., Chen F., Cheng J.F., Lucas S., Kerfeld C., Lang E., Gronow S., Chain P., Bruce D., Rubin E.M., Kyrpides N.C., Klenk H.P., Eisen J.A. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009, 462:1056-1060.
62. Yarza P., Yilmaz P., Prüße E., Glöckner F.O., Ludwig W., Schleifer K.-H., Whitman W.B., Euzéby J., Amann R., Rosselló-Móra.R. Uniting the classification of cultured and uncultured Bacteria and Archaea by means of SSU rRNA gene sequences. Nat. Microbiol. Rev. 2014, 12:635-645.