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

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Abstract

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).

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References

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Chimara E, Ferazoli L, Leão SC (2004) Mycobacterium tuberculosis complex differentiation using gyrB-restriction fragment length polymorphism analysis. Mem Inst Oswaldo Cruz 99:745–748

    PubMed  CAS  Google Scholar 

  • 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 49:1369–1373

    Article  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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 57:1747–1751

    Article  PubMed  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. doi:10.1007/BF01734359

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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 50:127–134

    PubMed  CAS  Google Scholar 

  • Keswani J, Whitman WB (2001) Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes. Int J Syst Evol Microbiol 51:667–678

    PubMed  CAS  Google Scholar 

  • 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 52:889–894

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Labeda DP (1995) Amycolatopsis coloradensis sp. nov., the avoparcin (LL-AV290)-producing strain. Int J Syst Bacteriol 45:124–127

    Google Scholar 

  • 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 36:29–37

    Google Scholar 

  • 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

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    PubMed  CAS  Google Scholar 

  • Sensi P, Greco AM, Ballotta R (1959) Rifomycin I isolation and properties of rifomycin B and rifomycin complex. Antibiot Annu 7:262–270

    PubMed  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340

    Google Scholar 

  • 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 44:846–849

    CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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 17:1251–1258

    PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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 37:463–464

    Article  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

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).

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  1. Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch, 7701, Cape Town, South Africa

    Gareth J. Everest & Paul R. Meyers

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  1. Gareth J. Everest
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  2. Paul R. Meyers
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Correspondence to Paul R. Meyers.

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The GenBank accession numbers for the gyrB gene sequences obtained in this study are shown in Table 1.

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Everest, G.J., Meyers, P.R. The use of gyrB sequence analysis in the phylogeny of the genus Amycolatopsis . Antonie van Leeuwenhoek 95, 1–11 (2009). https://doi.org/10.1007/s10482-008-9280-9

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  • DOI: https://doi.org/10.1007/s10482-008-9280-9

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