Antonie van Leeuwenhoek

, Volume 95, Issue 1, pp 1–11 | Cite as

The use of gyrB sequence analysis in the phylogeny of the genus Amycolatopsis

  • Gareth J. Everest
  • Paul R. Meyers
Original Paper


Partial gyrB sequences (>1 kb) were obtained from 34 type strains of the genus Amycolatopsis. Phylogenetic trees were constructed to determine the effectiveness of using this gene to predict taxonomic relationships within the genus. The use of gyrB sequence analysis as an alternative to DNA–DNA hybridization was also assessed for distinguishing closely related species. The gyrB based phylogeny mostly confirmed the conventional 16S rRNA gene-based phylogeny and thus provides additional support for certain of these 16S rRNA gene-based phylogenetic groupings. Although pairwise gyrB sequence similarity cannot be used to predict the DNA relatedness between type strains, the gyrB genetic distance can be used as a means to assess quickly whether an isolate is likely to represent a new species in the genus Amycolatopsis. In particular a genetic distance of >0.02 between two Amycolatopsis strains (based on a 315 bp variable region of the gyrB gene) is proposed to provide a good indication that they belong to different species (and that polyphasic taxonomic characterization of the unknown strain is worth undertaking).


Amycolatopsis DNA–DNA hybridization Genetic distance gyrB Phylogeny 



The authors would like to thank Di James for DNA sequencing. G.J.E. holds a grantholder-linked bursary from the National Research Foundation of South Africa (NRF), a Harry Crossley Foundation Postgraduate Scholarship from the University of Cape Town (UCT), a Twamley Postgraduate Bursary (UCT), a KW Johnstone Research Scholarship (UCT) and a Postgraduate Research Associateship (UCT). This work was supported by research grants to P.R.M. from the Medical Research Council of South Africa, the NRF (grant number: 2073133) and the University Research Committee (UCT).

Supplementary material

10482_2008_9280_MOESM1_ESM.doc (33 kb)
MOESM1 (DOC 33 kb).


  1. Al-Musallam AA, Al-Zarban SS, Fasasi YA, Kroppenstedt RM, Stackebrandt E (2003) Amycolatopsis keratiniphila sp. nov., a novel keratinolytic soil actinomycete from Kuwait. Int J Syst Evol Microbiol 53:871–874. doi: 10.1099/ijs.0.02515-0 PubMedCrossRefGoogle Scholar
  2. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402. doi: 10.1093/nar/25.17.3389 PubMedCrossRefGoogle Scholar
  3. Bala S, Khanna R, Dadhwal M, Prabagaran SR, Shivaji S, Cullum J et al (2004) Reclassification of Amycolatopsis mediterranei DSM 46095 as Amycolatopsis rifamycinica sp. nov. Int J Syst Evol Microbiol 54:1145–1149. doi: 10.1099/ijs.0.02901-0 PubMedCrossRefGoogle Scholar
  4. Chimara E, Ferazoli L, Leão SC (2004) Mycobacterium tuberculosis complex differentiation using gyrB-restriction fragment length polymorphism analysis. Mem Inst Oswaldo Cruz 99:745–748PubMedGoogle Scholar
  5. Chun J, Kim SB, Oh YK, Seong C-N, Lee D-H, Bae KS et al (1999) Amycolatopsis thermoflava sp. nov, a novel soil actinomycetes from Hainan Island, China. Int J Syst Evol Microbiol 49:1369–1373CrossRefGoogle Scholar
  6. Coenye T, Gevers D, Van de Peer Y, Vandamme P, Swings J (2005) Towards a prokaryotic genomic taxonomy. FEMS Microbiol Rev 29:147–167. doi: 10.1016/j.femsre.2004.11.004 PubMedCrossRefGoogle Scholar
  7. Ding L, Hirose T, Yokota A (2007) Amycolatopsis echigonensis sp. nov. and Amycolatopsis niigatensis sp. nov, novel actinomycetes isolated from filtration substrate. Int J Syst Evol Microbiol 57:1747–1751PubMedCrossRefGoogle Scholar
  8. Everest GJ, Meyers PR (2008) Kribbella hippodromi sp. nov., isolated from soil from a racecourse in South Africa. Int J Syst Evol Microbiol 58:443–446. doi: 10.1099/ijs.0.65278-0 PubMedCrossRefGoogle Scholar
  9. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. doi: 10.1007/BF01734359 PubMedCrossRefGoogle Scholar
  10. Jin J, Haga T, Shinjo T, Goto Y (2004) Phylogenetic analysis of Fusobacterium necrophorum, Fusobacterium varium and Fusobacterium nucleatum based on gyrB gene sequences. J Vet Med Sci 66:1243–1245. doi: 10.1292/jvms.66.1243 PubMedCrossRefGoogle Scholar
  11. Kasai H, Tamura T, Harayama S (2000) Intrageneric relationships among Micromonospora species deduced from gyrB-based phylogeny and DNA relatedness. Int J Syst Evol Microbiol 50:127–134PubMedGoogle Scholar
  12. Keswani J, Whitman WB (2001) Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes. Int J Syst Evol Microbiol 51:667–678PubMedGoogle Scholar
  13. Kim B, Sahin N, Tan GYA, Zakrzewska-Czerwinska J, Goodfellow M (2002) Amycolatopsis eurytherma sp. nov., a thermophilic actinomycetes isolated form soil. Int J Syst Evol Microbiol 52:889–894PubMedCrossRefGoogle Scholar
  14. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120. doi: 10.1007/BF01731581 PubMedCrossRefGoogle Scholar
  15. Labeda DP (1995) Amycolatopsis coloradensis sp. nov., the avoparcin (LL-AV290)-producing strain. Int J Syst Bacteriol 45:124–127Google Scholar
  16. Lechevalier MP, Prauser H, Labeda DP, Ruan JS (1986) Two new genera of nocardioform actinomycetes: Amycolata gen nov. and Amycolatopsis gen nov. Int J Syst Bacteriol 36:29–37Google Scholar
  17. le Roes M, Goodwin CM, Meyers PR (2008) Gordonia lacunae sp. nov. isolated from an estuary. Syst Appl Microbiol. doi: 10.1016/j.syapm.2007.10.001
  18. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  19. Sensi P, Greco AM, Ballotta R (1959) Rifomycin I isolation and properties of rifomycin B and rifomycin complex. Antibiot Annu 7:262–270PubMedGoogle Scholar
  20. Shen F-T, Lu H-L, Lin J-L, Huang W-S, Arun AB, Young C-C (2006) Phylogenetic analysis of members of the metabolically diverse genus Gordonia based on proteins encoding the gyrB gene. Res Microbiol 157:367–375. doi: 10.1016/j.resmic.2005.09.007 PubMedCrossRefGoogle Scholar
  21. Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340Google Scholar
  22. Stackebrandt E, Goebel BM (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 44:846–849Google Scholar
  23. 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 PubMedCrossRefGoogle Scholar
  24. Stackebrandt E, Kroppenstedt RM, Wink J, Schumann P (2004) Reclassification of Amycolatopsis orientalis subsp. lurida Lechevalier et al. 1986 as Amycolatopsis lurida sp. nov., comb nov. Int J Syst Evol Microbiol 54:267–268. doi: 10.1099/ijs.0.02937-0 PubMedCrossRefGoogle Scholar
  25. Takahashi K, Nei M (2000) Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol 17:1251–1258PubMedGoogle Scholar
  26. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599. doi: 10.1093/molbev/msm092 PubMedCrossRefGoogle Scholar
  27. Tan GY, Robinson S, Lacey E, Brown R, Kim W, Goodfellow M (2007) Amycolatopsis regifaucium sp. nov., a novel actinomycete that produces kigamicins. Int J Syst Evol Microbiol 57:2562–2567. doi: 10.1099/ijs.0.64974-0 PubMedCrossRefGoogle Scholar
  28. Thomson CJ, Power E, Ruebsamen-Waigmann H, Labischinski H (2004) Antibacterial research and development in the 21st Century—an industry perspective of the challenges. Curr Opin Microbiol 7:445–450. doi: 10.1016/j.mib.2004.08.009 PubMedCrossRefGoogle Scholar
  29. Watanabe K, Nelson JS, Harayama S, Kasai H (2001) ICB database: the gyrB database for identification and classification of bacteria. Nucleic Acids Res 29:344–345. doi: 10.1093/nar/29.1.344 PubMedCrossRefGoogle Scholar
  30. Wayne LG, Brenner DJ, Colwell RR et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464CrossRefGoogle Scholar
  31. Wink J, Kroppenstedt RM, Ganguli BM, Nadkarni SR, Schumann P, Seibert G et al (2003) Three new antibiotic producing species of the genus Amycolatopsis, Amycolatopsis balhimycina sp. nov., A. tolypomycina sp. nov., A. vancoresmycina sp. nov., and description of Amycolatopsis keratiniphila subsp. keratiniphila subsp. nov. and A. keratiniphila subsp. nogabecina subsp. nov. Syst Appl Microbiol 26:38–46. doi: 10.1078/072320203322337290 PubMedCrossRefGoogle Scholar
  32. Wink J, Gandhi J, Kroppenstedt RM, Seibert G, Straubler B, Schumann P et al (2004) Amycolatopsis decaplanina sp. nov., a novel member of the genus with unusual morphology. Int J Syst Evol Microbiol 54:235–239. doi: 10.1099/ijs.0.02586-0 PubMedCrossRefGoogle Scholar
  33. Zeigler DR (2003) Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53:1893–1900. doi: 10.1099/ijs.0.02713-0 PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  1. 1.Department of Molecular and Cell BiologyUniversity of Cape TownCape TownSouth Africa

Personalised recommendations