1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 64, Issue Pt_2

Integrating genomics into the taxonomy and systematics of the and Free

Abstract

The polyphasic approach used today in the taxonomy and systematics of the and includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the and coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

  • Published Online:
Funding
This study was supported by the:
  • National Research Foundation of the Republic of Korea (Award 2012M3A9D1054622 and 2013-035122)
© 2014 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.054171-0
2014-02-01
2024-04-16
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/2/316.html?itemId=/content/journal/ijsem/10.1099/ijs.0.054171-0&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. ( 1990 ). Basic local alignment search tool. . J Mol Biol 215, 403–410.[PubMed] [CrossRef]
    [Google Scholar]
  2. Amaral G. R. S., Dias G. M., Wellington-Oguri M., Chimetto L., Campeão M. E., Thompson F. L., Thompson C. C. ( 2014 ). Genotype to phenotype: identification of diagnostic vibrio phenotypes using whole genome sequences. . Int J Syst Evol Microbiol 64, 357–365.[PubMed] [CrossRef]
    [Google Scholar]
  3. Bentley D. R. ( 2006 ). Whole-genome re-sequencing. . Curr Opin Genet Dev 16, 545–552. [View Article] [PubMed]
    [Google Scholar]
  4. Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., Madden T. L. ( 2009 ). blast+: architecture and applications. . BMC Bioinformatics 10, 421. [View Article] [PubMed]
    [Google Scholar]
  5. Camelo-Castillo A., Benítez-Páez A., Belda-Ferre P., Cabrera-Rubio R., Mira A. ( 2014 ). Streptococcus dentisani sp. nov., a new member of the Mitis group. . Int J Syst Evol Microbiol 64 (in press [View Article] [PubMed]
    [Google Scholar]
  6. Chan J. Z.-M., Halachev M. R., Loman N. J., Constantinidou C., Pallen M. J. ( 2012 ). Defining bacterial species in the genomic era: insights from the genus Acinetobacter . . BMC Microbiol 12, 302. [View Article] [PubMed]
    [Google Scholar]
  7. Chun J., Grim C. J., Hasan N. A., Lee J. H., Choi S. Y., Haley B. J., Taviani E., Jeon Y. S., Kim D. W. & other authors ( 2009 ). Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae . . Proc Natl Acad Sci U S A 106, 15442–15447. [View Article] [PubMed]
    [Google Scholar]
  8. Cole J. R., Wang Q., Cardenas E., Fish J., Chai B., Farris R. J., Kulam-Syed-Mohideen A. S., McGarrell D. M., Marsh T. & other authors ( 2009 ). The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. . Nucleic Acids Res 37, D141–D145. [View Article] [PubMed]
    [Google Scholar]
  9. Colwell R. R. ( 1970 ). Polyphasic taxonomy of the genus Vibrio: numerical taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and related Vibrio species. . J Bacteriol 104, 410–433.[PubMed]
    [Google Scholar]
  10. Curtis T. P., Sloan W. T., Scannell J. W. ( 2002 ). Estimating prokaryotic diversity and its limits. . Proc Natl Acad Sci U S A 99, 10494–10499. [View Article] [PubMed]
    [Google Scholar]
  11. Deloger M., El Karoui M., Petit M. A. ( 2009 ). A genomic distance based on MUM indicates discontinuity between most bacterial species and genera. . J Bacteriol 191, 91–99. [View Article] [PubMed]
    [Google Scholar]
  12. Eid J., Fehr A., Gray J., Luong K., Lyle J., Otto G., Peluso P., Rank D., Baybayan P. & other authors ( 2009 ). Real-time DNA sequencing from single polymerase molecules. . Science 323, 133–138. [View Article] [PubMed]
    [Google Scholar]
  13. Fleischmann R. D., Adams M. D., White O., Clayton R. A., Kirkness E. F., Kerlavage A. R., Bult C. J., Tomb J. F., Dougherty B. A. & other authors ( 1995 ). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. . Science 269, 496–512. [View Article] [PubMed]
    [Google Scholar]
  14. 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. [View Article] [PubMed]
    [Google Scholar]
  15. Goris J., Konstantinidis K. T., Klappenbach J. A., Coenye T., Vandamme P., Tiedje J. M. ( 2007 ). DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. . Int J Syst Evol Microbiol 57, 81–91. [View Article] [PubMed]
    [Google Scholar]
  16. Guo Y., Zheng W., Rong X., Huang Y. ( 2008 ). A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics. . Int J Syst Evol Microbiol 58, 149–159. [View Article] [PubMed]
    [Google Scholar]
  17. Haley B. J., Grim C. J., Hasan N. A., Choi S. Y., Chun J., Brettin T. S., Bruce D. C., Challacombe J. F., Detter J. C. & other authors ( 2010 ). Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae . . BMC Microbiol 10, 154. [View Article] [PubMed]
    [Google Scholar]
  18. Henz S. R., Huson D. H., Auch A. F., Nieselt-Struwe K., Schuster S. C. ( 2005 ). Whole-genome prokaryotic phylogeny. . Bioinformatics 21, 2329–2335. [View Article] [PubMed]
    [Google Scholar]
  19. Hofer U. ( 2013 ). Environmental microbiology: exploring diversity with single-cell genomics. . Nat Rev Microbiol 11, 598–599. [View Article] [PubMed]
    [Google Scholar]
  20. Hoffmann M., Monday S. R., Allard M. W., Strain E. A., Whittaker P., Naum M., McCarthy P. J., Lopez J. V., Fischer M., Brown E. W. ( 2012 ). Vibrio caribbeanicus sp. nov., isolated from the marine sponge Scleritoderma cyanea . . Int J Syst Evol Microbiol 62, 1736–1743. [View Article] [PubMed]
    [Google Scholar]
  21. Jeon Y.-S., Lee K., Park S.-C., Kim B.-S., Cho Y.-J., Ha S.-M., Chun J. ( 2014 ). EzEditor: a versatile sequence alignment editor for both ribosomal RNA and protein coding genes. . Int J Syst Evol Microbiol 64 (in press). [CrossRef]
    [Google Scholar]
  22. Jiménez G., Urdiain M., Cifuentes A., López-López A., Blanch A. R., Tamames J., Kämpfer P., Kolstø A. B., Ramón D. & other authors ( 2013 ). Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group, and pairwise genome comparisons of the species of the group by means of ANI calculations. . Syst Appl Microbiol 36, 383–391. [View Article] [PubMed]
    [Google Scholar]
  23. Johnson J. L., Ordal E. J. ( 1968 ). Deoxyribonucleic acid homology in bacterial taxonomy: effect of incubation temperature on reaction specificity. . J Bacteriol 95, 893–900.[PubMed]
    [Google Scholar]
  24. Kent W. J. ( 2002 ). blat – the blast-like alignment tool. . Genome Res 12, 656–664.[PubMed] [CrossRef]
    [Google Scholar]
  25. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. & other authors ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716–721. [View Article] [PubMed]
    [Google Scholar]
  26. Kim M., Oh H.-S., Park S.-C., Chun J. ( 2014a ). Towards a taxanomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. . Int J Syst Evol Microbiol 64, 346–351. [View Article] [PubMed]
    [Google Scholar]
  27. Kim K. M., Park J.-H., Bhattacharya D., Yoon H. S. ( 2014b ). Applications of next-generation sequencing to unravelling the evolutionary history of algae. . Int J Syst Evol Microbiol 64, 333–345. [View Article] [PubMed]
    [Google Scholar]
  28. Konstantinidis K. T., Tiedje J. M. ( 2005 ). Genomic insights that advance the species definition for prokaryotes. . Proc Natl Acad Sci U S A 102, 2567–2572. [View Article] [PubMed]
    [Google Scholar]
  29. Koren S., Schatz M. C., Walenz B. P., Martin J., Howard J. T., Ganapathy G., Wang Z., Rasko D. A., McCombie W. R. & other authors ( 2012 ). Hybrid error correction and de novo assembly of single-molecule sequencing reads. . Nat Biotechnol 30, 693–700. [View Article] [PubMed]
    [Google Scholar]
  30. Kurtz S., Phillippy A., Delcher A. L., Smoot M., Shumway M., Antonescu C., Salzberg S. L. ( 2004 ). Versatile and open software for comparing large genomes. . Genome Biol 5, R12. [View Article] [PubMed]
    [Google Scholar]
  31. Kurtzman C. P. ( 2014 ). Use of gene sequence analyses and genome comparisons for yeast systematics. . Int J Syst Evol Microbiol 64, 325–332.[PubMed] [CrossRef]
    [Google Scholar]
  32. Lang J. M., Darling A. E., Eisen J. A. ( 2013 ). Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. . PLoS ONE 8, e62510. [View Article] [PubMed]
    [Google Scholar]
  33. Lee K., Park S. C., Yi H., Chun J. ( 2013 ). Flavobacterium limnosediminis sp. nov., isolated from sediment of a freshwater lake. . Int J Syst Evol Microbiol 63, 4784–4789. [View Article] [PubMed]
    [Google Scholar]
  34. Löffler F. E., Yan J., Ritalahti K. M., Adrian L., Edwards E. A., Konstantinidis K. T., Müller J. A., Fullerton H., Zinder S. H., Spormann A. M. ( 2013 ). Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi . . Int J Syst Evol Microbiol 63, 625–635. [View Article] [PubMed]
    [Google Scholar]
  35. Lucena T., Ruvira M. A., Arahal D. R., Macián M. C., Pujalte M. J. ( 2012 ). Vibrio aestivus sp. nov. and Vibrio quintilis sp. nov., related to Marisflavi and Gazogenes clades, respectively. . Syst Appl Microbiol 35, 427–431. [View Article] [PubMed]
    [Google Scholar]
  36. Maiden M. C., Bygraves J. A., Feil E., Morelli G., Russell J. E., Urwin R., Zhang Q., Zhou J., Zurth K. & other authors ( 1998 ). Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. . Proc Natl Acad Sci U S A 95, 3140–3145. [View Article] [PubMed]
    [Google Scholar]
  37. Margulies M., Egholm M., Altman W. E., Attiya S., Bader J. S., Bemben L. A., Berka J., Braverman M. S., Chen Y. J. & other authors ( 2005 ). Genome sequencing in microfabricated high-density picolitre reactors. . Nature 437, 376–380.[PubMed]
    [Google Scholar]
  38. Marrero G., Schneider K. L., Jenkins D. M., Alvarez A. M. ( 2013 ). Phylogeny and classification of Dickeya based on multilocus sequence analysis. . Int J Syst Evol Microbiol 63, 3524–3539. [View Article] [PubMed]
    [Google Scholar]
  39. Martens M., Delaere M., Coopman R., De Vos P., Gillis M., Willems A. ( 2007 ). Multilocus sequence analysis of Ensifer and related taxa. . Int J Syst Evol Microbiol 57, 489–503. [View Article] [PubMed]
    [Google Scholar]
  40. Meier-Kolthoff J. P., Auch A. F., Klenk H. P., Göker M. ( 2013 ). Genome sequence-based species delimitation with confidence intervals and improved distance functions. . BMC Bioinformatics 14, 60. [View Article] [PubMed]
    [Google Scholar]
  41. Meier-Kolthoff J. P., Klenk H.-P., Göker M. ( 2014 ). Taxanomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. . Int J Syst Evol Microbiol 64, 352–356. [View Article] [PubMed]
    [Google Scholar]
  42. Mende D. R., Sunagawa S., Zeller G., Bork P. ( 2013 ). Accurate and universal delineation of prokaryotic species. . Nat Methods 10, 881–884. [View Article] [PubMed]
    [Google Scholar]
  43. Naushad H. S., Lee B., Gupta R. S. ( 2014 ). Conserved signature indels and signature proteins as novel tools for understanding microbioal phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria . . Int J Syst Evol Microbiol 64, 366–383. [View Article] [PubMed]
    [Google Scholar]
  44. Oren A., Papke R. T. ( 2010 ). Molecular Phylogeny of Microorganisms. Wymondham, UK:: Caister Academic Press;.
     [Google Scholar]
  45. Ramasamy D., Mishra A. K., Lagier J.-C., Padhmanabhan R., Rossi M., Sentausa E., Raoult D., Fournier P.-E. ( 2014 ). A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. . Int J Syst Evol Microbiol 64, 384–391. [View Article] [PubMed]
    [Google Scholar]
  46. Richter M., Rosselló-Móra R. ( 2009 ). Shifting the genomic gold standard for the prokaryotic species definition. . Proc Natl Acad Sci U S A 106, 19126–19131. [View Article] [PubMed]
    [Google Scholar]
  47. Rinke C., Schwientek P., Sczyrba A., Ivanova N. N., Anderson I. J., Cheng J. F., Darling A., Malfatti S., Swan B. K. & other authors ( 2013 ). Insights into the phylogeny and coding potential of microbial dark matter. . Nature 499, 431–437. [View Article] [PubMed]
    [Google Scholar]
  48. Rosselló-Mora R. ( 2006 ). DNA-DNA reassociation methods applied to microbial taxonomy and their critical evaluation. . In Molecular Identification, Systematics and Population Structure of Prokaryotes, pp. 23–50. Edited by Stackebrandt E. . Berlin, Heidelberg:: Springer;. [View Article]
    [Google Scholar]
  49. Rosselló-Mora R., Amann R. ( 2001 ). The species concept for prokaryotes. . FEMS Microbiol Rev 25, 39–67. [View Article] [PubMed]
    [Google Scholar]
  50. Ruvira M. A., Lucena T., Pujalte M. J., Arahal D. R., Macián M. C. ( 2013 ). Marinifilum flexuosum sp. nov., a new Bacteroidetes isolated from coastal Mediterranean Sea water and emended description of the genus Marinifilum Na et al., 2009. . Syst Appl Microbiol 36, 155–159. [View Article] [PubMed]
    [Google Scholar]
  51. Sokal R. R., Sneath P. H. A. ( 1963 ). Principles of Numerical Taxonomy. San Francisco:: W. H. Freeman;.
     [Google Scholar]
  52. Stackebrandt E., Ebers J. ( 2006 ). Taxonomic parameters revisited: tarnished gold standards. . Microbiol Today 33, 152–155.
     [Google Scholar]
  53. Stackebrandt E., Goebel B. M. ( 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. [View Article]
    [Google Scholar]
  54. Stackebrandt E., Frederiksen W., Garrity G. M., Grimont P. A. D., Kämpfer P., Maiden M. C. J., Nesme X., Rosselló-Mora R., Swings J. & other authors ( 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. [View Article] [PubMed]
    [Google Scholar]
  55. Sullivan C. B., Diggle M. A., Clarke S. C. ( 2005 ). Multilocus sequence typing: data analysis in clinical microbiology and public health. . Mol Biotechnol 29, 245–254. [View Article] [PubMed]
    [Google Scholar]
  56. Swan B. K., Tupper B., Sczyrba A., Lauro F. M., Martinez-Garcia M., González J. M., Luo H., Wright J. J., Landry Z. C. & other authors ( 2013 ). Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. . Proc Natl Acad Sci U S A 110, 11463–11468. [View Article] [PubMed]
    [Google Scholar]
  57. Tindall B. J., Rosselló-Móra R., Busse H. J., Ludwig W., Kämpfer P. ( 2010 ). Notes on the characterization of prokaryote strains for taxonomic purposes. . Int J Syst Evol Microbiol 60, 249–266. [View Article] [PubMed]
    [Google Scholar]
  58. Vanlaere E., Baldwin A., Gevers D., Henry D., De Brandt E., LiPuma J. J., Mahenthiralingam E., Speert D. P., Dowson C., Vandamme P. ( 2009 ). Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species, Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov.. Int J Syst Evol Microbiol 59, 102–111. [View Article] [PubMed]
    [Google Scholar]
  59. 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. & other authors ( 1987 ). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37, 463–464. [View Article]
    [Google Scholar]
  60. Whitman W. B., Coleman D. C., Wiebe W. J. ( 1998 ). Prokaryotes: the unseen majority. . Proc Natl Acad Sci U S A 95, 6578–6583. [View Article] [PubMed]
    [Google Scholar]
  61. Wu D., Hugenholtz P., Mavromatis K., Pukall R., Dalin E., Ivanova N. N., Kunin V., Goodwin L., Wu M. & other authors ( 2009 ). A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea . . Nature 462, 1056–1060. [View Article] [PubMed]
    [Google Scholar]
  62. Yarza P., Spröer C., Swiderski J., Mrotzek N., Spring S., Tindall B. J., Gronow S., Pukall R., Klenk H. P. & other authors ( 2013 ). Sequencing orphan species initiative (SOS): filling the gaps in the 16S rRNA gene sequence database for all species with validly published names. . Syst Appl Microbiol 36, 69–73. [View Article] [PubMed]
    [Google Scholar]
  63. Yi H., Cho Y. J., Yoon S. H., Park S. C., Chun J. ( 2012 ). Comparative genomics of Neisseria weaveri clarifies the taxonomy of this species and identifies genetic determinants that may be associated with virulence. . FEMS Microbiol Lett 328, 100–105. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.054171-0
Loading
Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea
Int J Syst Evol Microbiol 64, 316 (2014); https://doi.org/10.1099/ijs.0.054171-0
/content/journal/ijsem/10.1099/ijs.0.054171-0
/content/journal/ijsem/10.1099/ijs.0.054171-0
Loading

Data & Media loading...

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error