Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA–DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species

International Journal of Systematic and Evolutionary Microbiology - Tập 60 Số 3 - Trang 696-703 - 2010
Xiaoying Rong1, Ying Huang1
1State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China

Tóm tắt

Streptomyces griseus and related species form the biggest but least well-defined clade in the whole Streptomyces 16S rRNA gene tree. Multilocus sequence analysis (MLSA) has shown promising potential for refining Streptomyces systematics. In this investigation, strains of 18 additional S. griseus clade species were analysed and data from a previous pilot study were integrated in a larger MLSA phylogeny. The results demonstrated that MLSA of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) is better than the previous six-gene scheme, as it provides equally good resolution and stability and is more cost-effective; MLSA using three or four of the genes also shows good resolution and robustness for differentiating most of the strains and is therefore of value for everyday use. MLSA is more suitable for discriminating strains that show >99 % 16S rRNA gene sequence similarity. DNA–DNA hybridization (DDH) between strains with representative MLSA distances revealed a strong correlation between the data of MLSA and DDH. The 70 % DDH value for current species definition corresponds to a five-gene MLSA distance of 0.007, which could be considered as the species cut-off for the S. griseus clade. It is concluded that the MLSA procedure can be a practical, reliable and robust alternative to DDH for the identification and classification of streptomycetes at the species and intraspecies levels. Based on the data from MLSA and DDH, as well as cultural and morphological characteristics, 18 species and three subspecies of the S. griseus clade are considered to be later heterotypic synonyms of 11 genomic species: Streptomyces griseinus and Streptomyces mediolani as synonyms of Streptomyces albovinaceus; Streptomyces praecox as a synonym of Streptomyces anulatus; Streptomyces olivoviridis as a synonym of Streptomyces atroolivaceus; Streptomyces griseobrunneus as a synonym of Streptomyces bacillaris; Streptomyces cavourensis subsp. washingtonensis as a synonym of Streptomyces cyaneofuscatus; Streptomyces acrimycini, Streptomyces baarnensis, Streptomyces caviscabies and Streptomyces flavofuscus as synonyms of Streptomyces fimicarius; Streptomyces flavogriseus as a synonym of Streptomyces flavovirens; Streptomyces erumpens, ‘Streptomyces ornatus’ and Streptomyces setonii as synonyms of Streptomyces griseus; Streptomyces graminofaciens as a synonym of Streptomyces halstedii; Streptomyces alboviridis, Streptomyces griseus subsp. alpha, Streptomyces griseus subsp. cretosus and Streptomyces luridiscabiei as synonyms of Streptomyces microflavus; and Streptomyces californicus and Streptomyces floridae as synonyms of Streptomyces puniceus.

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Tài liệu tham khảo

Achtman, 2008, Microbial diversity and the genetic nature of microbial species, Nat Rev Microbiol, 6, 431, 10.1038/nrmicro1872

Acinas, 2004, Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons, J Bacteriol, 186, 2629, 10.1128/JB.186.9.2629-2635.2004

Akaike, 1974, A new look at the statistical model identification, IEEE Trans Automat Contr, 19, 716, 10.1109/TAC.1974.1100705

Antony-Babu, 2008, Genetic and phenotypic evidence for Streptomyces griseus ecovars isolated from a beach and dune sand system, Antonie van Leeuwenhoek, 94, 63, 10.1007/s10482-008-9246-y

Chun, 1995, A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences, Int J Syst Bacteriol, 45, 240, 10.1099/00207713-45-2-240

Coenye, 2005, Towards a prokaryotic genomic taxonomy, FEMS Microbiol Rev, 29, 147, 10.1016/j.femsre.2004.11.004

Cohan, 2008, The origins of ecological diversity in prokaryotes, Curr Biol, 18, 1024, 10.1016/j.cub.2008.09.014

Ezaki, 1989, 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, Int J Syst Bacteriol, 39, 224, 10.1099/00207713-39-3-224

Felsenstein, 1985, Confidence limits on phylogenies: an approach using the bootstrap, Evolution, 39, 783, 10.1111/j.1558-5646.1985.tb00420.x

Felsenstein, 2008, phylip (phylogeny inference package) version 3.68. Distributed by the author. Department of Genome Sciences

Gevers, 2005, & other authors, Nat Rev Microbiol, 3, 733, 10.1038/nrmicro1236

Gevers, 2006, Stepping stones towards a new prokaryotic taxonomy, Philos Trans R Soc Lond B Biol Sci, 361, 1911, 10.1098/rstb.2006.1915

Guo, 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, 10.1099/ijs.0.65224-0

He, 2005, Streptomyces jietaisiensis sp. nov., isolated from soil in northern China, Int J Syst Evol Microbiol, 55, 1939, 10.1099/ijs.0.63460-0

Kämpfer, 2006, The family Streptomycetaceae . Part I. Taxonomy, In The Prokaryotes, vol, 538, 10.1007/0-387-30743-5_22

Kimura, 1980, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, J Mol Evol, 16, 111, 10.1007/BF01731581

Koeppel, 2008, Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics, Proc Natl Acad Sci U S A, 105, 2504, 10.1073/pnas.0712205105

Lanoot, 2005a, Grouping of streptomycetes using 16S-ITS RFLP fingerprinting, Res Microbiol, 156, 755, 10.1016/j.resmic.2005.01.017

Lanoot, 2005b

Lapage, 1992, International Code of Nomenclature of Bacteria: Bacteriological Code, 1990 Revision

Liu, 2005, Classification of Streptomyces griseus, Int J Syst Evol Microbiol, 55, 1605, 10.1099/ijs.0.63654-0

Martens, 2007, Multilocus sequence analysis of Ensifer and related taxa, Int J Syst Evol Microbiol, 57, 489, 10.1099/ijs.0.64344-0

Martens, 2008, Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium ), Int J Syst Evol Microbiol, 58, 200, 10.1099/ijs.0.65392-0

Mignard, 2008, A seven-gene, multilocus, genus-wide approach to the phylogeny of mycobacteria using supertrees, Int J Syst Evol Microbiol, 58, 1432, 10.1099/ijs.0.65658-0

Naser, 2006, Reclassification of Enterococcus flavescens Pompei et al. 1992 as a later synonym of Enterococcus casseliflavus ( ex Vaughan et al. 1979) Collins et al. 1984 and Enterococcus saccharominimus Vancanneyt et al. 2004 as a later synonym of Enterococcus italicus Fortina et al. 2004, Int J Syst Evol Microbiol, 56, 413, 10.1099/ijs.0.63891-0

Okanishi, 1972, An evaluation of taxonomic criteria in streptomycetes on the basis of deoxyribonucleic acid homology, J Gen Microbiol, 72, 49, 10.1099/00221287-72-1-49

Posada, 1998, Modeltest: testing the model of DNA substitution, Bioinformatics, 14, 817, 10.1093/bioinformatics/14.9.817

Rong, 2009, Proposal to reclassify the Streptomyces albidoflavus clade on the basis of multilocus sequence analysis and DNA–DNA hybridization, and taxonomic elucidation of Streptomyces griseus subsp. solvifaciens, Syst Appl Microbiol, 32, 314, 10.1016/j.syapm.2009.05.003

Rosselló-Mora, 2006, DNA-DNA reassociation methods applied to microbial taxonomy and their critical evaluation, In Molecular Identification, Systematics and Population Structure of Prokaryotes, 23, 10.1007/978-3-540-31292-5_2

Shirling, 1966, Methods for characterization of Streptomyces species, Int J Syst Bacteriol, 16, 313, 10.1099/00207713-16-3-313

Stackebrandt, 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, 10.1099/00207713-44-4-846

Stackebrandt, 2002, Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology, Int J Syst Evol Microbiol, 52, 1043

Swofford, 2002, paup*: Phylogenetic analysis using parsimony (and other methods), version 4

Tamura, 2007, mega4: molecular evolutionary genetics analysis (mega) software version 4.0, Mol Biol Evol, 24, 1596, 10.1093/molbev/msm092

Vandamme, 1996, Polyphasic taxonomy, a consensus approach to bacterial systematics, Microbiol Rev, 60, 407, 10.1128/MMBR.60.2.407-438.1996

Wayne, 1987, International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics, Int J Syst Bacteriol, 37, 463, 10.1099/00207713-37-4-463

Wu, 2008, Taxonomic study of a chromomycin-producing strain and reclassification of Streptomyces cavourensis subsp. washingtonensis as a later synonym of Streptomyces griseus, Int J Syst Evol Microbiol, 58, 2783, 10.1099/ijs.0.65628-0

Young, 2008, A multilocus sequence analysis of the genus Xanthomonas, Syst Appl Microbiol, 31, 366, 10.1016/j.syapm.2008.06.004

Zeigler, 2003, Gene sequences useful for predicting relatedness of whole genomes in bacteria, Int J Syst Evol Microbiol, 53, 1893, 10.1099/ijs.0.02713-0

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Thông tin xuất bản

International Journal of Systematic and Evolutionary Microbiology

Tập 60 Số 3

696-703

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