Whole-genome analyses: Average nucleotide identity

Methods in Microbiology

Volumn 41, Issue , 2014, Pages 103-122

  Arahal, David R ^a  

^a UNIVERSITY OF VALENCIA   (Spain)

Author keywords

Average nucleotide identity; Comparative genomics; DNA DNA hybridization; Prokaryotic systematics; Whole genome analyses

Indexed keywords

EID: 84919421321     PISSN: 05809517     EISSN: None     Source Type: Book Series    
DOI: 10.1016/bs.mim.2014.07.002     Document Type: Chapter

References (65)

1. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., et al. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research 1997, 25:3389-3402.
2. Arahal D.R., Sánchez E., Macián M.C., Garay E. Value of recN sequences for species identification and as a phylogenetic marker within the family "Leuconostocaceae". International Microbiology 2008, 11:33-39.
3. Bakermans C., Ayala-del-Río H.L., Ponder M.A., Vishnivetskaya T., Gilichinsky D., Thomashow M.F., et al. Psychrobacter cryohalolentis sp. nov. and Psychrobacter arcticus sp. nov., isolated from Siberian permafrost. International Journal of Systematic and Evolutionary Microbiology 2006, 56:1285-1291.
4. Ben Zakour N.L., Beatson S.A., van den Broek A.H., Thoday K.L., Fitzgerald J.R. Comparative genomics of the Staphylococcus intermedius group of animal pathogens. Frontiers in Cellular and Infection Microbiology 2012, 2:44.
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. Borriss R., Rueckert C., Blom J., Bezuidt O., Reva O., Klenk H.-P. Whole genome sequence comparisons in taxonomy. Methods in microbiology 2011, Vol. 38:409-436. Academic Press, London.
7. Camelo-Castillo A., Benítez-Páez A., Belda-Ferre P., Cabrera-Rubio R., Mira A. Streptococcus dentisani sp. nov. a novel member of the Mitis group. International Journal of Systematic and Evolutionary Microbiology 2014, 64:60-65.
8. Campbell M.A., Chain P.S., Dang H., El Sheikh A.F., Norton J.M., Ward N.L., et al. Nitrosococcus watsonii sp. nov., a new species of marine obligate ammonia-oxidizing bacteria that is not omnipresent in the world's oceans: Calls to validate the names 'Nitrosococcus halophilus' and 'Nitrosomonas mobilis'. FEMS Microbiology Ecolology 2011, 76:39-48.
9. Chan J.Z., Halachev M.R., Loman N.J., Constantinidou C., Pallen M.J. Defining bacterial species in the genomic era: Insights from the genus Acinetobacter. BMC Microbiology 2012, 12:302.
10. Chi W.J., Park J.S., Kwak M.J., Kim J.F., Chang Y.K., Hong S.K. Isolation and characterization of a novel agar-degrading marine bacterium, Gayadomonas joobiniege gen. nov, sp. nov., from the Southern Sea, Korea. Journal of Microbiology and Biotechnology 2013, 23:1509-1518.
11. Cho Y.J., Yi H., Chun J., Cho S.N., Daley C.L., Koh W.J., et al. The genome sequence of 'Mycobacterium massiliense' strain CIP 108297 suggests the independent taxonomic status of the Mycobacterium abscessus complex at the subspecies level. PLoS One 2013, 8:e81560.
12. Chun J., Rainey F.A. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. International Journal of Systematic and Evolutionary Microbiology 2014, 64:316-324.
13. Dark M.J. Whole-genome sequencing in bacteriology: State of the art. Infection and Drug Resistance 2013, 6:115-123.
14. Delamuta J.R., Ribeiro R.A., Ormeño-Orrillo E., Melo I.S., Martínez-Romero E., Hungria M. Polyphasic evidence supporting the reclassification of Bradyrhizobium japonicum group Ia strains as Bradyrhizobium diazoefficiens sp. nov. International Journal of Systematic and Evolutionary Microbiology 2013, 63:3342-3351.
15. Deloger M., El Karoui M., Petit M.A. A genomic distance based on MUM indicates discontinuity between most bacterial species and genera. Journal of Bacteriology 2009, 191:91-99.
16. den Bakker H.C., Manuel C.S., Fortes E.D., Wiedmann M., Nightingale K.K. Genome sequencing identifies Listeria fleischmannii subsp. coloradonensis subsp. nov., isolated from a ranch. International Journal of Systematic and Evolutionary Microbiology 2013, 63:3257-3268.
17. Ezaki T., Hashimoto Y., Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane-filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. International Journal of Systematic Bacteriology 1989, 39:224-229.
18. Flowers J.J., He S., Malfatti S., Del Rio T.G., Tringe S.G., Hugenholtz P., et al. Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removal. ISME Journal 2013, 7:2301-2314.
19. Frank C.S., Klockow C., Richter M., Glöckner F.O., Harder J. Genetic diversity of Rhodopirellula strains. Antonie Van Leeuwenhoek 2013, 104:547-550.
20. García-Aljaro C., Ballesté E., Rosselló-Móra R., Cifuentes A., Richter M., Blanch A.R. Neoscardovia arbecensis gen. nov., sp. nov., isolated from porcine slurries. Systematic and Applied Microbiology 2012, 35:374-379.
21. 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. International Journal of Systematic and Evolutionary Microbiology 2007, 57:81-91.
22. Guinebretière M.H., Auger S., Galleron N., Contzen M., De Sarrau B., De Buyser M.L., et al. Bacillus cytotoxicus sp. nov. is a novel thermotolerant species of the Bacillus cereus group occasionally associated with food poisoning. International Journal of Systematic and Evolutionary Microbiology 2013, 63:31-40.
23. Haley B.J., Grim C.J., Hasan N.A., Choi S.Y., Chun J., Brettin T.S., et al. Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae. BMC Microbiology 2010, 10:154.
24. Hamilton-Brehm S.D., Mosher J.J., Vishnivetskaya T., Podar M., Carroll S., Allman S., et al. Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park. Applied and Environmental Microbiology 2010, 76:1014-1020.
25. Hoffmann M., Monday S.R., Allard M.W., Strain E.A., Whittaker P., Naum M., et al. Vibrio caribbeanicus sp. nov., isolated from the marine sponge Scleritoderma cyanea. International Journal of Systematic and Evolutionary Microbiology 2012, 62:1736-1743.
26. Jiménez G., Urdiain M., Cifuentes A., López-López A., Blanch A.R., Tamames J., et al. 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. Systematic and Applied Microbiology 2013, 36:383-391.
27. Jores J., Fischer A., Sirand-Pugnet P., Thomann A., Liebler-Tenorio E.M., Schnee C., et al. Mycoplasma feriruminatoris sp. nov., a fast growing Mycoplasma species isolated from wild Caprinae. Systematic and Applied Microbiology 2013, 36:533-538.
28. 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. International Journal of Systematic and Evolutionary Microbiology 2014, 64:346-351.
29. Konstantinidis K.T., Ramette A., Tiedje J.M. Toward a more robust assessment of intraspecies diversity, using fewer genetic markers. Applied and Environmental Microbiology 2006, 72:7286-7293.
30. Konstantinidis K.T., Tiedje J.M. Genomic insights that advance the species definition for prokaryotes. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:2567-2572.
31. Kurtz S., Phillippy A., Delcher A.L., Smoot M., Shumway M., Antonescu C., et al. Versatile and open software for comparing large genomes. Genome Biology 2004, 5:R12.
32. Lebedeva E.V., Hatzenpichler R., Pelletier E., Schuster N., Hauzmayer S., Bulaev A., et al. 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.
33. Lee K., Park S.C., Yi H., Chun J. Flavobacterium limnosediminis sp. nov., isolated from sediment of a freshwater lake. International Journal of Systematic and Evolutionary Microbiology 2013, 63:4784-4789.
34. Liu L., Li Y., Li S., Hu N., He Y., Pong R., et al. Comparison of next-generation sequencing systems. Journal of Biomedicine and Biotechnology 2012, 2012:251364.
35. Liu B., Liu G.H., Hu G.P., Sengonca C., Lin N.Q., Tang J.Y., et al. Bacillus bingmayongensis sp. nov., isolated from the pit soil of Emperor Qin's Terra-cotta warriors in China. Antonie Van Leeuwenhoek 2014, 105:501-510.
36. Löffler F.E., Yan J., Ritalahti K.M., Adrian L., Edwards E.A., Konstantinidis K.T., et al. 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. International Journal of Systematic and Evolutionary Microbiology 2013, 63:625-635.
37. Loman N.J., Misra R.V., Dallman T.J., Constantinidou C., Gharbia S.E., Wain J., et al. Performance comparison of benchtop high-throughput sequencing platforms. Nature Biotechnology 2012, 30:434-439.
38. Lü Z., Lu Y. Methanocella conradii sp. nov., a thermophilic, obligate hydrogenotrophic methanogen, isolated from Chinese rice field soil. PLoS One 2012, 7:e35279.
39. Lucena T., Ruvira M.A., Arahal D.R., Macián M.C., Pujalte M.J. Vibrio aestivus sp. nov. and Vibrio quintilis sp. nov., related to Marisflavi and Gazogenes clades, respectively. Systematic and Applied Microbiology 2012, 35:427-431.
40. Lucena T., Ruvira M.A., Macián M.C., Pujalte M.J., Arahal D.R. Description of Tropicibacter mediterraneus sp. nov. and Tropicibacter litoreus sp. nov. Systematic and Applied Microbiology 2013, 36:325-329.
41. Lucena T., Ruvira M.A., Macián M.C., Pujalte M.J., Arahal D.R. Roseovarius albus sp. nov., a new Alphaproteobacterium isolated from the Mediterranean Sea. Antonie Van Leeuwenhoek 2014, 105:671-678.
42. Matsumoto A., Kasai H., Matsuo Y., Shizuri Y., Ichikawa N., Fujita N., et al. Ilumatobacter nonamiense sp. nov. and Ilumatobacter coccineum sp. nov., isolated from seashore sand. International Journal of Systematic and Evolutionary Microbiology 2013, 63:3404-3408.
43. Mavromatis K., Land M.L., Brettin T.S., Quest D.J., Copeland A., Clum A., et al. The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation. PLoS One 2012, 7:e48837.
44. Mesbah N.M., Whitman W.B., Mesbah M. Determination of the G+C content of prokaryotes. Methods in microbiology 2011, Vol. 38:299-324. Academic Press, London.
45. Nemec A., Krizova L., Maixnerova M., van der Reijden T.J., Deschaght P., Passet V., et al. Genotypic and phenotypic characterization of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex with the proposal of Acinetobacter pittii sp. nov. (formerly Acinetobacter genomic species 3) and Acinetobacter nosocomialis sp. nov. (formerly Acinetobacter genomic species 13TU). Research in Microbiology 2011, 162:393-404.
46. Nesbø C.L., Bradnan D.M., Adebusuyi A., Dlutek M., Petrus A.K., Foght J., et al. Mesotoga prima gen. nov., sp. nov., the first described mesophilic species of the Thermotogales. Extremophiles 2012, 16:387-393.
47. Prakash O., Gihring T.M., Dalton D.D., Chin K.J., Green S.J., Akob D.M., et al. Geobacter daltonii sp. nov., an Fe(III)- and uranium(VI)-reducing bacterium isolated from a shallow subsurface exposed to mixed heavy metal and hydrocarbon contamination. International Journal of Systematic and Evolutionary Microbiology 2010, 60:546-553.
48. Quail M.A., Smith M., Coupland P., Otto T.D., Harris S.R., Connor T.R., et al. A tale of three next generation sequencing platforms: Comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 2012, 13:341.
49. Richter M., Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:19126-19131.
50. Romano C., D'Imperio S., Woyke T., Mavromatis K., Lasken R., Shock E.L., et al. Comparative genomic analysis of phylogenetically closely related Hydrogenobaculum sp. isolates from Yellowstone National Park. Applied and Environmental Microbiology 2013, 79:2932-2943.
51. Rosselló-Móra R., Urdiain M., López-López A. DNA-DNA hybridization. Methods in microbiology 2011, Vol. 38:325-347. Academic Press, London.
52. Ruvira M.A., Lucena T., Pujalte M.J., Arahal D.R., Macián M.C. Marinifilum flexuosum sp. nov., a new Bacteroidetes isolated from coastal Mediterranean Sea water and emended description of the genus Marinifilum Na et al., 2009. Systematic and Applied Microbiology 2013, 36:155-159.
53. Saw J.H., Schatz M., Brown M.V., Kunkel D.D., Foster J.S., Shick H., et al. Cultivation and complete genome sequencing of Gloeobacter kilaueensis sp. nov., from a lava cave in Kīlauea Caldera, Hawai'i. PLoS One 2013, 8:e76376.
54. Scortichini M., Marcelletti S., Ferrante P., Firrao G. A genomic redefinition of Pseudomonas avellanae species. PLoS One 2013, 8:e75794.
55. Sentausa E., Fournier P.E. Advantages and limitations of genomics in prokaryotic taxonomy. Clinical Microbiology and Infection 2013, 19:790-795.
56. Stackebrandt E., Frederiksen W., Garrity G.M., Grimont P.A., Kämpfer P., Maiden M.C., et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. International Journal of Systematic and Evolutionary Microbiology 2002, 52:1043-1047.
57. Tamura T., Matsuzawa T., Oji S., Ichikawa N., Hosoyama A., Katsumata H., et al. A genome sequence-based approach to taxonomy of the genus Nocardia. Antonie Van Leeuwenhoek 2012, 102:481-491.
58. Tindall B.J., Rosselló-Móra R., Busse H.J., Ludwig W., Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. International Journal of Systematic and Evolutionary Microbiology 2010, 60:249-266.
59. Tomás A.F., Karakashev D., Angelidaki I. Thermoanaerobacter pentosaceus sp. nov., an anaerobic, extremely thermophilic, high ethanol-yielding bacterium isolated from household waste. International Journal of Systematic and Evolutionary Microbiology 2013, 63:2396-2404.
60. van der Wolf J.M., Nijhuis E.H., Kowalewska M.J., Saddler G.S., Parkinson N., Elphinstone J.G., et al. Dickeya solani sp. nov., a pectinolytic plant pathogenic bacterium isolated from potato (Solanum tuberosum). International Journal of Systematic and Evolutionary Microbiology 2014, 64:768-774.
61. Vanlaere E., Baldwin A., Gevers D., Henry D., De Brandt E., LiPuma J.J., et al. Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species. Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov. International Journal of Systematic and Evolutionary Microbiology 2009, 59:102-111.
62. Villeneuve C., Martineau C., Mauffrey F., Villemur R., Villeneuve C., Martineau C., et al. Methylophaga nitratireducenticrescens sp. nov. and Methylophaga frappieri sp. nov., isolated from the biofilm of the methanol-fed denitrification system treating the seawater at the Montreal Biodome. International Journal of Systematic and Evolutionary Microbiology 2013, 63:2216-2222.
63. Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler O., Krichevsky M.I., et al. International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. International Journal of Systematic Bacteriology 1987, 37:463-464.
64. Yi H., Chun J., Cha C.J. Genomic insights into the taxonomic status of the three subspecies of Bacillus subtilis. Systematic and Applied Microbiology 2014, 37:95-99.
65. Zhang Y.M., Tian C.F., Sui X.H., Chen W.F., Chen W.X. Robust markers reflecting phylogeny and taxonomy of rhizobia. PLoS One 2012, 7:e44936.