1887

Abstract

Over recent years, genomic information has increasingly been used for prokaryotic species definition and classification. Genome sequence-based alternatives to the gold standard DNA–DNA hybridization (DDH) relatedness have been developed, notably average nucleotide identity (ANI), which is one of the most useful measurements for species delineation in the genomic era. However, the strictly intracellar lifestyle, the few measurable phenotypic properties and the low level of genetic heterogeneity made the current standard genomic criteria for bacterial species definition inapplicable to species. We evaluated a range of whole genome sequence (WGS)-based taxonomic parameters to develop guidelines for the classification of isolates at genus and species levels. By comparing the degree of similarity of 74 WGSs from 31 species and 61 WGSs from members of three closely related genera also belonging to the order (, 11 genomes; , 22 genomes; and , 28 genomes) using digital DDH (dDDh) and ANI by orthology (OrthoANI) parameters, we demonstrated that WGS-based taxonomic information, which is easy to obtain and use, can serve for reliable classification of isolates within the genus and species. To be classified as a member of the genus , a bacterial isolate should exhibit OrthoANI values with any species with a validly published name of ≥83.63 %. To be classified as a new species, an isolate should not exhibit more than any of the following degrees of genomic relatedness levels with the most closely related species: >92.30 and >99.19 % for the dDDH and OrthoANI values, respectively. When applied to four rickettsial isolates of uncertain status, the above-described thresholds enabled their classification as new species in one case. Thus, we propose WGS-based guidelines to efficiently delineate species, with OrthoANI and dDDH being the most accurate for classification at the genus and species levels, respectively.

Funding
This study was supported by the:
  • Fondation Méditerranée Infection (Award None)
    • Principle Award Recipient: Awa Diop
  • Agence Nationale de la Recherche (Award 10-IAHU-03)
    • Principle Award Recipient: Didier Raoult
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003963
2020-01-14
2024-12-08
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/3/1738.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003963&mimeType=html&fmt=ahah

References

  1. Da Rocha-Lima H. Zur Aetiologie des Fleckfiebers. Berl Klin Wochenschr 1916; 53:567–569
    [Google Scholar]
  2. Ngwamidiba M, Raoult D, Fournier PE. Rickettsia: history and current position. Antibiotiques 2006; 8:117–131
    [Google Scholar]
  3. Weiss E, Moulder JW, Order I. Rickettsiales Gieszczkiewicz 1939. In Bergey DH, Krieg NR, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology Baltimore, MD: Williams & Wilkins; 1984 pp 687–703
    [Google Scholar]
  4. Skerman VBD, Sneath PHA, McGowan V. Approved lists of bacterial names. Int J Syst Evol Microbiol 1980; 30:225–420 [View Article]
    [Google Scholar]
  5. Raoult D, Roux V. Rickettsioses as paradigms of new or emerging infectious diseases. Clin Microbiol Rev 1997; 10:694–719 [View Article]
    [Google Scholar]
  6. Weisburg WG, Dobson ME, Samuel JE, Dasch GA, Mallavia LP et al. Phylogenetic diversity of the rickettsiae. J Bacteriol 1989; 171:4202–4206 [View Article]
    [Google Scholar]
  7. Fournier P-E, Raoult D. Current knowledge on phylogeny and taxonomy of Rickettsia spp. Ann N Y Acad Sci 2009; 1166:1–11 [View Article]
    [Google Scholar]
  8. Neimark H, Johansson KE, Rikihisa Y, Tully JG. Proposal to transfer some members of the genera Haemobartonella and Eperythrozoon to the genus Mycoplasma with descriptions of 'Candidatus Mycoplasma haemofelis', 'Candidatus Mycoplasma haemomuris', 'Candidatus Mycoplasma haemosuis' and 'Candidatus Mycoplasma wenyonii'. Int J Syst Evol Microbiol 2001; 51:891–899 [View Article]
    [Google Scholar]
  9. Roux V, Bergoin M, Lamaze N, Raoult D. Reassessment of the taxonomic position of Rickettsiella grylli . Int J Syst Bacteriol 1997; 47:1255–1257 [View Article]
    [Google Scholar]
  10. Birtles RJ, Harrison TG, Saunders NA, Molyneux DH. Proposals to unify the genera Grahamella and Bartonella, with descriptions of Bartonella talpae comb, nov., Bartonella peromysci comb. nov., and three new species, Bartonella grahamii sp. nov., Bartonella taylorii sp. nov., and Bartonella doshiae sp. nov. Int J Syst Bacteriol 1995; 45:1–8 [View Article]
    [Google Scholar]
  11. Brenner DJ, O'Connor SP, Winkler HH, Steigerwalt AG. Proposals to unify the genera Bartonella and Rochalimaea, with descriptions of Bartonella quintana comb. nov., Bartonella vinsonii comb. nov., Bartonella henselae comb. nov., and Bartonella elizabethae comb. nov., and to remove the family Bartonellaceae from the order Rickettsiales . Int J Syst Bacteriol 1993; 43:777–786 [View Article]
    [Google Scholar]
  12. Tamura A, Ohashi N, Urakami H, Miyamura S. Classification of Rickettsia tsutsugamushi in a new genus, Orientia gen. nov., as Orientia tsutsugamushi comb. nov. Int J Syst Bacteriol 1995; 45:589–591 [View Article]
    [Google Scholar]
  13. Dumler JS, Barbet AF, Bekker C, Dasch GA, Palmer GH et al. Reorganization of genera in the families Rickettsiaceae and Anaplasmataceae in the order Rickettsiales: unification of some species of Ehrlichia with Anaplasma, Cowdria with Ehrlichia and Ehrlichia with Neorickettsia, descriptions of six new species combinations and designation of Ehrlichia equi and 'HGE agent' as subjective synonyms of Ehrlichia phagocytophila. Int J Syst Evol Microbiol 2001; 51:2145–2165 [View Article]
    [Google Scholar]
  14. Drancourt M, Raoult D. Taxonomic position of the rickettsiae: current knowledge. FEMS Microbiol Rev 1994; 13:13–24 [View Article]
    [Google Scholar]
  15. Fournier P-E, Dumler JS, Greub G, Zhang J, Wu Y et al. Gene sequence-based criteria for identification of new Rickettsia isolates and description of Rickettsia heilongjiangensis sp. nov. J Clin Microbiol 2003; 41:5456–5465 [View Article]
    [Google Scholar]
  16. Philip RN, Casper EA, Burgdorfer W, Gerloff RK, Hughes LE et al. Serologic typing of rickettsiae of the spotted fever group by microimmunofluorescence. J Immunol 1978; 121:1961–1968
    [Google Scholar]
  17. Gillespie JJ, Beier MS, Rahman MS, Ammerman NC, Shallom JM et al. Plasmids and rickettsial evolution: insight from Rickettsia felis . PLoS One 2007; 2:e266 [View Article]
    [Google Scholar]
  18. Grimont PAD. Use of DNA reassociation in bacterial classification. Can J Microbiol 1988; 34:541–546 [View Article]
    [Google Scholar]
  19. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  20. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article]
    [Google Scholar]
  21. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article]
    [Google Scholar]
  22. Parker CT, Tindall BJ, Garrity GM. International Code of Nomenclature of prokaryotes. Int J Syst Evol Microbiol 2019; 69:S1–S111
    [Google Scholar]
  23. Chan JZ-M, Halachev MR, Loman NJ, Constantinidou C, Pallen MJ. Defining bacterial species in the genomic era: insights from the genus Acinetobacter . BMC Microbiol 2012; 12:302 [View Article]
    [Google Scholar]
  24. Padmanabhan R, Mishra AK, Raoult D, Fournier P-E. Genomics and metagenomics in medical microbiology. J Microbiol Methods 2013; 95:415–424 [View Article]
    [Google Scholar]
  25. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the bacteria and archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article]
    [Google Scholar]
  26. Klenk H-P, Meier-Kolthoff JP, Göker 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
    [Google Scholar]
  27. Meier-Kolthoff JP, Göker M, Spröer C, Klenk H-P. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article]
    [Google Scholar]
  28. Klappenbach JA, Goris J, Vandamme P, Coenye T, Konstantinidis KT et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91
    [Google Scholar]
  29. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article]
    [Google Scholar]
  30. 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 [View Article]
    [Google Scholar]
  31. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article]
    [Google Scholar]
  32. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article]
    [Google Scholar]
  33. Chung M, Munro JB, Tettelin H, Dunning Hotopp JC, Hotopp JCD. Using core genome alignments to assign bacterial species. mSystems 2018; 3:21 [View Article]
    [Google Scholar]
  34. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article]
    [Google Scholar]
  35. Lechner M, Findeiß S, Steiner L, Marz M, Stadler PF et al. Proteinortho: Detection of (Co-)orthologs in large-scale analysis. BMC Bioinformatics 2011; 12:124 [View Article]
    [Google Scholar]
  36. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article]
    [Google Scholar]
  37. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article]
    [Google Scholar]
  38. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article]
    [Google Scholar]
  39. Auch AF, 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 Genomic Sci 2010; 2:117–134 [View Article]
    [Google Scholar]
  40. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [View Article]
    [Google Scholar]
  41. Gillespie JJ, Joardar V, Williams KP, Driscoll T, Hostetler JB et al. A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyle. J Bacteriol 2012; 194:376–394 [View Article]
    [Google Scholar]
  42. Padgett KA, Bonilla D, Eremeeva ME, Glaser C, Lane RS et al. The eco-epidemiology of Pacific coast tick fever in California. PLoS Negl Trop Dis 2016; 10:e0005020 [View Article]
    [Google Scholar]
  43. Murray GGR, Weinert LA, Rhule EL, Welch JJ. The phylogeny of Rickettsia using different evolutionary signatures: how tree-like is bacterial evolution?. Syst Biol 2016; 65:265–279 [View Article]
    [Google Scholar]
  44. Davis GE, Parker RR. Comparative experiments on spotted fever and Boutonneuse fever (I). Public Health Rep 1934; 49:423–428 [View Article]
    [Google Scholar]
  45. Pickens EG, Bell EJ, Lackman DB, Burgdorfer W. Use of mouse serum in identification and serologic classification of Rickettsia akari and Rickettsia australis . J Immunol 1965; 94:883–889
    [Google Scholar]
  46. Lackman DB, Bell EJ, Stoenner HG, Pickens EG. The Rocky Mountain spotted fever group of rickettsias. Health Lab Sci 1965; 2:135–141
    [Google Scholar]
  47. Walker DH, Li H, Taylor C, Liu QH, Yu XJ et al. Antigenic diversity of Rickettsia conorii . Am J Trop Med Hyg 1992; 47:78–86 [View Article]
    [Google Scholar]
  48. Xu W, Raoult D. Taxonomic relationships among spotted fever group rickettsiae as revealed by antigenic analysis with monoclonal antibodies. J Clin Microbiol 1998; 36:887–896
    [Google Scholar]
  49. Merhej V, Raoult D. Rickettsial evolution in the light of comparative genomics. Biol Rev 2011; 86:379–405 [View Article]
    [Google Scholar]
  50. Garrity GM. A new genomics-driven taxonomy of bacteria and archaea: are we there yet?. J Clin Microbiol 2016; 54:1956–1963 [View Article]
    [Google Scholar]
  51. Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article]
    [Google Scholar]
  52. Gupta A, Sharma VK. Using the taxon-specific genes for the taxonomic classification of bacterial genomes. BMC Genomics 2015; 16:396 [View Article]
    [Google Scholar]
  53. Thompson CC, Vieira NM, Vicente ACP, Thompson FL. Towards a genome based taxonomy of Mycoplasmas . Infect Genet Evol 2011; 11:1798–1804 [View Article]
    [Google Scholar]
  54. Rosselló-Mora R, Amann R. The species concept for prokaryotes. FEMS Microbiol Rev 2001; 25:39–67 [View Article]
    [Google Scholar]
  55. Parola P, Paddock CD, Socolovschi C, Labruna MB, Mediannikov O et al. Update on tick-borne rickettsioses around the world: a geographic approach. Clin Microbiol Rev 2013; 26:657–702 [View Article]
    [Google Scholar]
  56. Zhu Y, Fournier P-E, Eremeeva M, Raoult D. Proposal to create subspecies of Rickettsia conorii based on multi-locus sequence typing and an emended description of Rickettsia conorii . BMC Microbiol 2005; 5:11 [View Article]
    [Google Scholar]
  57. Alowaysi M, Chen J, Stark S, Teague K, LaCourse M et al. Isolation and characterization of a Rickettsia from the ovary of a Western black-legged tick, Ixodes pacificus . Ticks Tick Borne Dis 2019; 10:918–923 [View Article]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.003963
Loading
/content/journal/ijsem/10.1099/ijsem.0.003963
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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