Evaluation of the antibiotic biosynthetic potential of the genus Amycolatopsis and description of Amycolatopsis circi sp. nov., Amycolatopsis equina sp. nov. and Amycolatopsis hippodromi sp. nov

Journal of Applied Microbiology

Volumn 111, Issue 2, 2011, Pages 300-311

  Everest, G J ^a   Meyers, P R ^a  

^a UNIVERSITY OF CAPE TOWN   (South Africa)

Author keywords

Antibiotic biosynthetic potential; Family Pseudonocardiaceae; Fynbos; gyrB genetic distance; Nocardioform actinomycetes; Rapid genus identification

Indexed keywords

BIOSYNTHESIS; GENES; RNA;

16S RRNA GENE; ANTIBIOTIC BIOSYNTHETIC POTENTIAL; FAMILY PSEUDONOCARDIACEAE; FYNBOS; GENETIC DISTANCES; GYRB GENES; GYRB GENETIC DISTANCE; NOCARDIOFORM ACTINOMYCETE; PHYLOGENETIC ANALYSIS; RAPID GENUS IDENTIFICATION;

ANTIBIOTICS;

ANSAMYCIN DERIVATIVE; ANTIBIOTIC AGENT; AVOPARCIN; DNA TOPOISOMERASE (ATP HYDROLYSING) B; GENOMIC DNA; RNA 16S;

ANTIBIOTICS; GENOMICS; HYBRIDIZATION; NEW GENUS; NEW SPECIES; PHYLOGENETICS;

AMYCOLATOPSIS ALBA; AMYCOLATOPSIS ALBIDOFLAVUS; AMYCOLATOPSIS AUSTRALIENSIS; AMYCOLATOPSIS AZUREA; AMYCOLATOPSIS BALHIMYCINA; AMYCOLATOPSIS BENZOATILYTICA; AMYCOLATOPSIS CIRCI; AMYCOLATOPSIS COLORADENSIS; AMYCOLATOPSIS DECAPLANINA; AMYCOLATOPSIS ECHIGONENSIS; AMYCOLATOPSIS EQUINA; AMYCOLATOPSIS EURYTHERMA; AMYCOLATOPSIS HALOPHILA; AMYCOLATOPSIS HALOTOLERANS; AMYCOLATOPSIS HELVEOLA; AMYCOLATOPSIS HIPPODROMI; AMYCOLATOPSIS JAPONICA; AMYCOLATOPSIS JEJUENSIS; AMYCOLATOPSIS KENTUCKYENSIS; AMYCOLATOPSIS KERATINIPHILA; AMYCOLATOPSIS LEXINGTONENSI; AMYCOLATOPSIS LURIDA; AMYCOLATOPSIS MARINA; AMYCOLATOPSIS METHANOLICA; AMYCOLATOPSIS MINNESOTENSIS; AMYCOLATOPSIS NIGRESCENS; AMYCOLATOPSIS NIIGATENSIS; AMYCOLATOPSIS PALATOPHARYNGIS; AMYCOLATOPSIS PIGMENTATA; AMYCOLATOPSIS PLUMENSIS; AMYCOLATOPSIS PRETORIENSIS; AMYCOLATOPSIS REGIFAUCIUM; AMYCOLATOPSIS RIFAMYCINICA; AMYCOLATOPSIS RUBIDA; AMYCOLATOPSIS SAALFELDENSIS; AMYCOLATOPSIS SACCHARI; AMYCOLATOPSIS SAMANEAE; AMYCOLATOPSIS TAIWANENSIS; AMYCOLATOPSIS THAILANDENSIS; AMYCOLATOPSIS THERMOFLAVA; AMYCOLATOPSIS TOLYPOMYCINA; AMYCOLATOPSIS TUCUMANENSIS; AMYCOLATOPSIS ULTIMINOTIA; AMYCOLATOPSIS VANCORESMYCINA; AMYCOLATOPSIS XYLANICA; ANTIBIOTIC BIOSYNTHESIS; ARTICLE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; DNA HYBRIDIZATION; ESCHERICHIA COLI; GENETIC ANALYSIS; MYCOBACTERIUM AURUM; NOCARDIA MEDITERRANEA; NOCARDIA ORIENTALIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PARSIMONY ANALYSIS; PHYLOGENETIC TREE; PHYLOGENY; PSEUDONOCARDIACEAE; SACCHAROPOLYSPORA; STAPHYLOCOCCUS AUREUS; UNINDEXED SEQUENCE;

ACTINOBACTERIA (CLASS); AMYCOLATOPSIS; PSEUDONOCARDIACEAE;

EID: 79960564561     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/j.1365-2672.2011.05058.x     Document Type: Article

References (37)

1. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.
2. Atlas, R.M. (2004) Handbook of Microbiological Media (3rd edition). Boca Raton, FL: CRC Press.
3. Bala, S., Khanna, R., Dadhwal, M., Prabagaran, S.R., Shivaji, S., Cullum, J. and Lal, R. (2004) Reclassification of Amycolatopsis mediterranei DSM 46095 as Amycolatopsis rifamycinica sp. nov. Int J Syst Evol Microbiol 54, 1145-1149.
4. Chen, J., Su, J.J., Wei, Y.Z., Li, Q.P., Yu, L.Y., Liu, H.Y., Zhang, Y.Q. and Zhang, Y.Q. (2010) Amycolatopsis xylanica sp. nov., isolated from soil. Int J Syst Evol Microbiol 60, 2124-2128.
5. Cook, A.E. and Meyers, P.R. (2003) Rapid identification of filamentous actinomycetes to the genus level using genus-specific 16S-rRNA gene restriction fragment patterns. Int J Syst Evol Microbiol 53, 1907-1915.
6. De Ley, J., Cattoir, H. and Reynaerts, A. (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 133-142.
7. Ding, L., Hirose, T. and Yokota, A. (2007) Amycolatopsis echigonensis sp. nov. and Amycolatopsis niigatensis sp. nov., novel actinomycetes isolated from a filtration substrate. Int J Syst Evol Microbiol 57, 1747-1751.
8. Everest, G.J. and Meyers, P.R. (2008) Kribbella hippodromi sp. nov., isolated from soil from a racecourse in South Africa. Int J Syst Evol Microbiol 58, 443-446.
9. Everest, G.J. and Meyers, P.R. (2009) The use of gyrB sequence analysis in the phylogeny of the genus Amycolatopsis. Antonie Van Leeuwenhoek 95, 1-11.
10. Hamaki, T., Suzuki, M., Fudou, R., Jojima, Y., Kajiura, T., Tabuchi, A., Sen, K. and Shibai, H. (2005) Isolation of novel bacteria and actinomycetes using Soil-Extract Agar medium. J Biosci Bioeng 99, 485-492.
11. Hamedi, J., Mohammadipanah, F., Klenk, H.-P., Pötter, G., Schumann, P., Spröer, C., Von Jan, M. and Kroppenstedt, R.M. (2010) Streptomyces iranensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 60, 1504-1509.
12. Hasegawa, T., Takizawa, M. and Tanida, S. (1983) A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29, 319-322.
13. Huang, Y., Qi, W., Lu, Z., Liu, Z. and Goodfellow, M. (2001) Amycolatopsis rubida sp. nov., a new Amycolatopsis species from soil. Int J Syst Evol Microbiol 51, 1093-1097.
14. Huss, V.A.R., Festl, H. and Schleifer, K.H. (1983) Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4, 184-192.
15. 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.
16. Komagata, K. and Suzuki, K.L. (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161-207.
17. Lechevalier, M.P., Prauser, H., Labeda, D.P. and Ruan, J.S. (1986) Two new genera of nocardioform actinomycetes: Amycolata gen. nov. and Amycolatopsis gen. nov. Int J Syst Bacteriol 36, 29-37.
18. Lee, S.D. (2006) Amycolatopsis jejuensis sp. nov. and Amycolatopsis halotolerans sp. nov., novel actinomycetes isolated from a natural cave. Int J Syst Evol Microbiol 56, 549-553.
19. Lee, S.D. and Hah, Y.C. (2001) Amycolatopsis albidoflavus sp. nov. Int J Syst Evol Microbiol 51, 645-650.
20. Minnikin, D.E., Alshamaony, L. and Goodfellow, M. (1975) Differentiation of Mycobacterium, Nocardia, and related taxa by think-layer chromatographic analysis of whole-organism methanolysates. J Gen Microbiol 88, 200-204.
21. Minnikin, D.E., O'Donnell, A.G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A. and Parlett, J.H. (1984) An integrated procedure for the extraction of bacterial isoprenoid quinines and polar lipids. J Microbiol Methods 2, 233-241.
22. Nonomura, H. and Ohara, Y. (1971) Distribution of actinomycetes in soil. VIII. Green spore group of Microtetraspora, its preferential isolation and taxonomic characteristics. J Ferment Technol 49, 1-7.
23. Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
24. Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989) Bacterial media, antibiotics and bacterial strains. In Molecular Cloning, a Laboratory Manual, 2nd edn. Cold Spring Harbor: Cold Spring Harbor Laboratory Press.
25. Shirling, E.B. and Gottlieb, D. (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313-340.
26. Takahashi, K. and 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.
27. Tamura, K., Dudley, J., Nei, M. and Kumar, S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24, 1596-1599.
28. Tamura, T., Ishida, Y., Otoguro, M. and Suzuki, K. (2010) Amycolatopsis helveola sp. nov. and Amycolatopsis pigmentata sp. nov., isolated from soil. Int J Syst Evol Microbiol 60, 2629-2633.
29. Tan, G.Y.A., Ward, A.C. and Goodfellow, M. (2006) Exploration of Amycolatopsis diversity in soil using genus-specific primers and novel selective media. Syst Appl Microbiol 29, 557-569.
30. Tang, S.K., Wang, Y., Guan, T.W., Lee, J.C., Kim, C.J. and Li, W.J. (2010) Amycolatopsis halophila sp. nov., a halophilic actinomycete isolated from a salt lake. Int J Syst Evol Microbiol 60, 1073-1078.
31. 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. et al. (1987) Report of the d hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463-464.
32. AL. In Bergey's Manual of Systematic Bacteriology, Vol. 4 ed. Williams, S.T., Sharpe, M.E. and Holt, J.G. pp. 2452-2492. Baltimore: Williams and Wilkins.
33. Wink, J., Kroppenstedt, R.M., Ganguli, B.M., Nadkarni, S.R., Schumann, P., Seibert, G. and Stackenbrandt, E. (2003a) 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.
34. Wink, J., Kroppenstedt, R.M., Seibert, G. and Stackebrandt, E. (2003b) Actinomadura namibiensis sp. nov. Int J Syst Evol Microbiol 53, 721-724.
35. Wink, J., Gandhi, J., Kroppenstedt, R.M., Seibert, G., Straubler, B., Schumann, P. and Stackebrandt, E. (2004) Amycolatopsis decaplanina sp. nov., a novel member of the genus with unusual morphology. Int J Syst Evol Microbiol 54, 235-239.
36. Wood, S.A., Kirby, B.M., Goodwin, C.M., le Roes, M. and Meyers, P.R. (2007) PCR screening reveals unexpected antibiotic biosynthetic potential in Amycolatopsis sp. strain UM16. J Appl Microbiol 102, 245-253.
37. Zhi, X.-Y., Li, W.-J. and Stackebrandt, E. (2009) An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 59, 589-608.