Phylogenetic study of the species within the family Streptomycetaceae

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 101, Issue 1, 2012, Pages 73-104

  Labeda, D P ^a   Goodfellow, M ^b   Brown, R ^b   Ward, A C ^b   Lanoot, B ^c   Vanncanneyt, M ^c   Swings, J ^c   Kim, S B ^d   Liu, Z ^e   Chun, J ^f   Tamura, T ^g   Oguchi, A ^g   Kikuchi, T ^g   Kikuchi, H ^g   Nishii, T ^g   Tsuji, K ^g   Yamaguchi, Y ^g   Tase, A ^g   Takahashi, M ^g   Sakane, T ^g   Suzuki, K I ^g   Hatano, K ^g   more..

^a NATIONAL CENTER FOR AGRICULTURAL UTILIZATION RESEARCH   (United States)

^b NEWCASTLE UNIVERSITY   (United Kingdom)

^c GHENT UNIVERSITY   (Belgium)

^d Chungnam National University   (South Korea)

^e INSTITUTE OF MICROBIOLOGY   (China)

^f Seoul National University   (South Korea)

^g NATIONAL INSTITUTE OF TECHNOLOGY AND EVALUATION   (Japan)

Author keywords

Actinobacteria; Actinomycetes; Streptomycetales; Systematics

Indexed keywords

16S RRNA GENE; BACTERIAL STRAIN; BOOTSTRAPPING; CLADISTICS; CONFERENCE PAPER; GENE SEQUENCE; GENOME ANALYSIS; KITASATOSPORA; MOLECULAR PHYLOGENY; MULTILOCUS SEQUENCE TYPING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; RNA GENE; SPECIES DIVERSITY; STREPTACIDIPHILUS; STREPTOMYCETACEAE; TAXONOMY; UNINDEXED SEQUENCE;

CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; STREPTOMYCETACEAE;

ACTINOBACTERIA; ACTINOBACTERIA (CLASS); STREPTOMYCES; STREPTOMYCETACEAE;

EID: 84856234790     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-011-9656-0     Document Type: Conference Paper

References (65)

1. A co-operative study, Gottlieb D (1961) An evaluation of criteria and procedures used in the description and characterization of the streptomycetes. Appl Microbiol 9:55-65
2. Anderson AS, Wellington EMH (2001) The taxonomy of Streptomyces and related genera. Int J Syst Evol Microbiol 51:797-814 (Pubitemid 32505652)
3. Bouchek-Mechiche K, Gardan L, Andrivon D, Normand P (2006) Streptomyces turgidiscabies and Streptomyces reticuliscabiei: one genomic species, two pathogenic groups. Int J Syst Evol Microbiol 56:2771-2776 (Pubitemid 44970986)
4. Chun J, Goodfellow M (1995) A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45:240-245
5. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
6. Felsenstein J (1993) Phylogeny inference package (PHYLIP) version 3.5. University of Washington, Seattle
7. Ferguson EV, Ward AC, Sanglier J-J, Goodfellow M (1997) Evaluation of Streptomyces species-groups by pyrolysis mass spectrometry. Zbl Bakt 285:169-181
8. Goodfellow M, Williams ST, Alderson G (1986a) Transfer of Elytrosporangium brasiliense Falcão de Morais et al., Elytrosporangium spirale Falcão de Morais et al., Microellobosporia flava Cross et al., Microellobosporia grisea (Konev et al.) Pridham and Microellobosporia violacea (Tsyganov et al.) Pridham to the genus Streptomyces, with emended descriptions of the species. Syst Appl Microbiol 8:48-54
9. Goodfellow M, Williams ST, Alderson G (1986b) Transfer of Chainia species to the genus Streptomyces with emended description of species. Syst Appl Microbiol 8:55-60
10. Goodfellow M, Williams ST, Alderson G (1986c) Transfer of Actinosporangium violaceum Krasil'nikov and Yuan, Actinosporangium vitaminophilum Shomura et al. and Actinopycridium caeruleum Krasil'nikov to the genus Streptomyces, with emended descriptions of the species. Syst Appl Microbiol 8:61-64
11. Goodfellow M, Williams ST, Alderson G (1986d) Transfer of Kitasatoa purpurea Matsumae and Hata to the genus Streptomyces as Streptomyces purpureus comb. nov. Syst Appl Microbiol 8:65-66
12. Goodfellow M, Ferguson EV, Sanglier J-J (1992) Numerical classification and identification of Streptomyces species-a review. Gene 115:225-233
13. Goodfellow M, Kumar Y, Labeda DP, Sembiring L (2007) The Streptomyces violaceusniger clade: a home for streptomycetes with rugose ornamented spores. Antonie van Leeuwenhoek 92:173-197
14. Gottlieb D (1963) Recommendations for description of some Actinomycetales appearing in patent applications. Int Bull Bacteriol Nomencl Taxon 13:159-160
15. Guo Y, Zheng W, Rong X, Huang Y (2008) A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics. Int J Syst Evol Microbiol 58:149-159 (Pubitemid 351843556)
16. Hall TA (1999) BioEdit, a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/ NT. Nucleic Acids Symp Ser 41:95-98
17. AL emend. Witt and Stackebrandt 1990, 370, emend. Wellington, Stackebrandt, Sanders, Wolstrup and Jorgensen, 1992, 159. In: Goodfellow M, Kämpfer P, Busse H-J, Trujillo M, Suzuki KE, Ludwig W, Whitman WB (eds) Bergey's Manual of Systematic Bacteriology, 2nd edn, volume 5 Springer, USA (in press)
18. Kämpfer P, Kroppenstedt RM, Dott W (1991) A numerical classification of the genera Streptomyces and Streptoverticillium using miniaturized physiological tests. J Gen Microbiol 137:1831-1891
19. Kim D, Chun J, Sahin N, Hah YC, Goodfellow M (1996) Analysis of thermophilic clades within the genus Streptomyces by 16S ribosomal DNA sequence comparisons. Int J Syst Bacteriol 46:581-587 (Pubitemid 26113888)
20. Kim SB, Lonsdale JT, Seong C-N, Goodfellow M (2003) Streptacidiphilus gen. nov., a home for acidiphilic actinomycetes with a wall chemotype 1 and emendation of the family Streptomycetaceae (Waksman & Henrici 1943 emend Rainey et al. 1997) Antonie van Leeuwenhoek 83:107-116 (Pubitemid 36592751)
21. Krainsky A (1914) Die Aktinomyceten und ihren Bedeutung in der Natur. Zentrlbl Bakteriol Parasiterikd Infektionkr Hyg II Abt 41:649-688
22. Kumar Y, Goodfellow M (2008) Five new members of the Streptomyces violaceusniger 16S rRNA gene clade: Streptomyces castelarensis comb. nov., S. himastatinicus sp. nov., S. mordarskii sp. nov., S. rapamycinicus sp. nov. and S. ruanii sp. nov. Int J Syst Evol Microbiol 58: 1369-1378
23. Kumar Y, Goodfellow M (2010) Reclassification of Streptomyces hygroscopicus strains as Streptomyces aldersoniae sp. nov., Streptomyces augustmyceticus sp. nov., comb. nov., Streptomyces ascomycinicus sp. nov. Streptomyces decoyicus sp. nov., comb. nov., Streptomyces milbemycinicus sp. nov. and Streptomyces wellingtoniae sp. nov. Int J Syst Evol Microbiol 60:769-775
24. Küster E (1959) Outline of a comparative study of criteria used in characterization of the actinomycetes. Int Bull Bacteriol Nomencl Taxon 9:97-104
25. Labeda DP (1992) DNA:DNA hybridization in the systematics of Streptomyces. Gene 115:249-253
26. Labeda DP (1993) DNA:DNA relatedness among strains of the Streptomyces lavendulae phenotypic cluster group. Int J Syst Evol Microbiol 53:822-825 (Pubitemid 23299839)
27. Labeda DP (1998) DNA:DNA relatedness among the Streptomyces fulvissimus and Streptomyces griseoviridis phenotypic cluster groups. Int J Syst Evol Microbiol 48:829-832 (Pubitemid 28394663)
28. Labeda DP (2011) Multilocus sequence analysis of phytopathogenic Streptomyces species. Int J Syst Evol Microbiol 61:2379-2383
29. Labeda D, Kroppenstedt RM (2000) Phylogenetic analysis of Saccharothrix and related taxa: proposal for Actinosynnemataceae fam. nov. Int J Syst Evol Microbiol 50:331-336 (Pubitemid 30084088)
30. Labeda DP, Lyons AJ (1991a) Deoxyribonucleic acid relatedness among species of the "Streptomyces cyaneus" cluster. Syst Appl Microbiol 14:158-164
31. Labeda DP, Lyons AJ (1991b) The Streptomyces violaceusniger cluster is heterogeneous in DNA relatedness among strains: emendation of the descriptions of S. violaceusniger and Streptomyces hygroscopicus. Int J Syst Bacteriol 41:398-401
32. Labeda DP, Price NP, Kroppenstedt RM, Donahue JM, Williams NM, Sells SF (2009) Streptomyces atriruber sp. nov. and Streptomyces silaceus sp. nov., two novel species of equine origin. Int J Syst Evol Microbiol 59:2899-2903
33. Lu Z, Liu Z, Wang L, Zhang Y, Qi W, Goodfellow M (2001) Saccharopolyspora flava sp. nov. and Saccharopolyspora thermophila sp. nov., novel actinomycetes from soil. Int J Syst Evol Microbiol 51:319-325 (Pubitemid 32266674)
34. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Buchner A, Yadhukumar Lai, Steppi S et al (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371 (Pubitemid 38854737)
35. Manchester L, Pot B, Kersters K, Goodfellow M (1990) Classification of Streptomyces and Streptoverticillium species by numerical analysis of electrophoretic protein patters. Syst Appl Microbiol 13:333-337
36. Mordarski M, Goodfellow M, Williams ST, Sneath PHA (1986) Evaluation of species groups in the genus Streptomyces. In: Szabó G, Biró S, Goodfellow M (eds) Biological, biochemical and biomedical aspects of actinomycetes. Akademiai Kiadó, Budapest, pp 517-525
37. Omura S, Takahashi Y, Iwai Y, Tamaka H (1982) Kitasatosporia, a new genus of the order Actinomycetales. J Antibiot 35:1013-1019 (Pubitemid 13241419)
38. Park MS, Jung SR, Lee MS, Kim KO, Do JO, Lee KH, Kim SB, Bae KS (2005) Isolation and characterization of bacteria associated with two sand dune plant species, Calystegia soldanella and Elymus mollis. J Microbiol 43:219-227
39. Pridham TG, Tresner HD (1974) Genus I. Streptomyces Waksman and Henrici 1943, 339. In: Buchanan RE, Gibbons NE (eds) Bergey's Manual of Determinative Bacteriology, 8th edn edn. Williams and Wilkins Company, Baltimore, pp 748-829
40. Ridell M, Wallerstrom G, Williams ST (1986) Immunodiffusion analysis of phenetically defined strains of Streptomyces, Streptoverticillium and Nocardiopsis. Syst Appl Microbiol 8:24-27
41. Rong X, Huang Y (2010) Taxonomic evaluation of the Streptomyces griseus clade using mulitilocus sequence analysis and DNA-DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species. Int J Syst Evol Microbiol 60:696-703
42. Rong X, Gou Y, Huang Y (2009) Proposal to reclassify the Streptomyces albidoflavus clade based on the basis of multilocus sequence analysis and DNA-DNA hybridization, and taxonomic elucidation of Streptomyces griseus subsp solvifaciens. Syst Appl Microbiol 32:314-322
43. Saddler GS, O'Donnell AG, Goodfellow M, Minnikin DE (1987) SIMCA pattern recognition in the analysis of streptomycete fatty acids. J Gen Microbiol 133:1137-1147 (Pubitemid 17086129)
44. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
45. Schatz A, Bugie E, Waksman SA (1944) Streptomycin, a substance inhibiting antibiotic activity against gram-positive and gram-negative bacteria. Proc Soc Exp Biol Med 55: 66-69
46. Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313-340
47. Shirling EB, Gottlieb D (1968a) Cooperative description of type cultures of Streptomyces. II. Species descriptions from first study. Int J Syst Bacteriol 38:69-189
48. Shirling EB, Gottlieb D (1968b) Cooperative description of type cultures of Streptomyces. III. Additional species descriptions from first and second studies. Int J Syst Bacteriol 18:279-292
49. Shirling EB, Gottlieb (1969) Cooperative description of type cultures of Streptomyces. IV. Species descriptions from the second, third and fourth studies. Int J Syst Bacteriol 19:391-512
50. Shirling EB, Gottlieb D (1972) Cooperative description of type strains of Streptomyces V. Additional descriptions. Int J Syst Bacteriol 22:265-394
51. Sneath PHA (1970) Application of numerical taxonomy to Actinomycetales: problems and perspectives. In: Prauser H (ed) The Actinomycetales. Gustav Fischer, Jena, pp 371-378
52. Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today Nov 06: 152-155
53. Tamura K, NeiM(1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512-526 (Pubitemid 23157236)
54. Tamura T, Ishida Y, Otoguro M, Hatano K, Suzuki K (2008a) Classification of 'Streptomyces tenebrarius' Higgins and Kastner as Streptoalloteichus tenebrarius nom. rev., comb. nov., and emended description of the genus Streptoalloteichus. Int J Syst Evol Microbiol 58:688-691
55. Tamura T, Ishida Y, Otoguro M, Hatano K, Labeda D, Price NP, Suzuki K (2008b) Reclassification of Streptomyces caeruleus as a synonym of Actinoalloteichus cyanogriseus and reclassification of Streptomyces spheroides and Streptomyces laceyi as later synonyms of Streptomyces niveus. Int J Syst Evol Microbiol 58:2812-2813
56. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using likelihood, distance, and parsimony methods. Mol Biol Evol 28 (in press)
57. Trejo WH (1970) An evaluation of some concepts and criteria used in the speciation of streptomycetes. Trans NY Acad Sci Ser II 32:989-997
58. Waksman SA (1919) Cultural studies of species of Actinomyces. Soil Sci 8:71-215
59. Waksman SA, Curtis RE (1916) The actinomycetes of the soil. Soil Sci 1:99-134
60. Waksman SA, Woodruff HB (1941) Actinomycetes antibioticus, a new soil organism antagonistic to pathogenic and nonpathogenic bacteria. J Bacteriol 42:231-249
61. Williams ST, Goodfellow M, Alderson G, Wellington EMH, Sneath PHA, SackinMJ (1983) Numerical classification of Streptomyces and related genera. J Gen Microbiol 129: 1743-1813 (Pubitemid 13044278)
62. Williams ST, Goodfellow M, Alderson G (1989) Genus Streptomyces Waksman and Henrici 1943, 339AL. In: Williams ST, Sharpe ME, Holt JG (eds) Bergey's manual of determinative bacteriology, volume 4. Williams and Wilkins, Baltimore, pp 2453-2492
63. AL. Syst Appl Microbiol 13:361-371
64. Xu C, Wang W, Cui Q, Huang Y, Liu Z, Zheng G, Goodfellow M (2006) Neutrotolerant acidiphilic Streptomyces species isolated from acidic-soils in China: Streptomyces guanduensis sp. nov., Streptomyces paucisporeus sp. nov., Streptomyces rubidus sp. nov. and Streptomyces yanglinensis sp. nov. Int J Syst Evol Microbiol 56:1109-1115 (Pubitemid 43820841)
65. Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer K-H, Ludwig W, Glöckner FO, Roselló-Móra R (2008) The all-species living tree project: a 16S rRNA-based phylogenetic tree for all sequenced type strains. Sys Appl Microbiol 31:241-250