kjcm-15-79

Korean J Clin Microbiol Vol. 15, No. 3, September, 2012http://dx.doi.org/10.5145/KJCM.2012.15.3.79

Basic Concepts of Bacterial TaxonomyYoung Sook Kim1, Sook-Jin Jang2

Departments of 1Radiology, and 2Laboratory Medicine, Chosun University College of Medicine, Gwangju, Korea

The three components of taxonomy are classification, nomenclature and identification. Traditionally, bacte-rial classification and identification were performed based on the morphology and the biochemical data of the bacteria. In newer theories, or so-called natu-ral concepts, the relationships between bacteria are based on the overall similarities of both the pheno-typic and genotypic characteristics. The polyphasic taxonomy, or current taxonomy, describes the in-tegration of all of the available genotypic, phenotypic, and phylogenetic information into a consensus type of general-purpose classification. When routine identi-

fication methods that are based on the biochemical tests fail, alternative procedures such as complete 16s rRNA gene sequence analysis are required. Although the results of 16s rRNA gene sequence analysis have not been fully discriminatory to differ-entiate closely related species, they may guide the additional analyses that are required for species identification. (Korean J Clin Microbiol 2012;15:79-87)

Key Words: Bacteria, Classification, Identification, rRNA genes, Taxonomy

Received 11 February, 2012, Revised 14 March, 2012Accepted 25 March, 2012Correspondence: Sook-Jin Jang, Department of Laboratory Medicine,

Chosun University Hospital, 588 Seoseok-dong, Dong-gu, Gwangju 501-717, Korea. (Tel) 82-62-220-3272, (Fax) 82-62-232-2063, (E-mail) [email protected]

79

(systematics) (classifi-cation), (nomenclature) (identification) . (similarity) (taxo-nomic group) . [1]. .

1.

. . . (phenetics)

[2]. . . . 1) : . . . , . . (numerical) . (chemotaxonomic) (genotypic) .1987 Ad Hoc , [3]. - DNA- DNA(whole-genome DNA-DNA hybridization) .

80 Korean J Clin Microbiol 2012;15(3):79-87

DNA-DNA 70% Tm 5oC ( ) . Tm (hybrid) Tm . Tm (homologous hybrid) (heterologous hybrid) Tm( ) [4]. DNA-DNA . . DNA-DNA (DNA-DNA hybridization) . DNA-DNA . (genomic species) genomo-var [5]. 2) (polyphasic) : Colwell[6] (polyphasic taxonomy) , , (chemotaxonomic), .

DNA DNA (base) (genome size), , , . rRNA (fraction) [7]. (mycolic acid), , , (sugars), polyamines, qui-nones, (, , ) [1]. , rRNA (signature features) . ATPase beta subunit, elongation factor Tu, chaperonin, , RNA polymerase tRNA [7,8]. . DNA-DNA . . . Bordetella per-

tussis B. parapertussis B. bronchiseptica DNA- DNA 80% [9]. Acidovorax (genera) DNA-DNA 40% [10]. . Wayne DNA-DNA . [4]. . DNA- DNA , 16S rRNA . . (genus) (family), (order) (ranks) . 16S rRNA . 3) : (prokaryotic) . , , , , . [11,12]. . , , , , , (nucleotide signature composition) , (metabolic pathway reaction content anal-yses) . (multilo-cus sequence analysis, MLSA)

Young Sook Kim and Sook-Jin Jang : Basic Concepts of Bacterial Taxonomy 81

Fig. 1. Schematic diagram showing procedure of multilocus sequence analysis (MLSA). The concatenated sequences of seven house keeping genes (HKG) are used for phylogenticanalysis of four species of bacteria to improve species descriptions in this figure.

. MLSA (multilocus se-quence typing, MLST) 4-10 (housekeeping gene) DNA . PCR . MLST , MLSA [13]. MLST , MLSA (genera) . MLST . (allelic profiles) . . MLST (downstream analyses) . MLSA DNA . MLSA [13] (Fig. 1). 16S rRNA . (phylogenetic

backbone) 16S rRNA (intraspecies) [1].

2.

, , . (DNA RNA) , (chemo-taxonomic markers) . , . 1) (1) DNA-DNA : DNA-DNA . DNA-DNA (DNA-DNA hybridization) DNA . DNA . . DNA DNA . ()(heteroduplex) (thermal stabil-ity) (genetic diverge-


Fig. 2. Schematic diagram showing DNA-DNA hybridization procedure. (A) The DNA-DNA hybridization step. The DNA of two species ofbacteria are heated and mixed together. During incubation, the DNA strands were dissociated and reannealed forming three kinds of hybrid double-stranded DNAs, (B) the melting procedure to analyze the melting profile of the hybridized DNA. The double-stranded DNA is bound to a column and the mixture is heated in small steps.

nce) [14]. , DNA DNA . DNA DNA (hybrid double-stranded DNA) . . DNA . DNA column . column . . DNA column . (homologous hybrid) (heterologous hybrid) Tm Tm DNA DNA [14] (Fig. 2). . . . DNA-DNA , , .

[15]. . DNA-DNA . , DNA-DNA , DNA-DNA , DNA-DNA . DNA-DNA . DNA-DNA (cut off) . . DNA-DNA DNA-DNA . (2) rRNA : rRNA (target) . 16S 23S rRNA PCR (direct sequencing) . [16,17]. (conserved elements) . rRNA motifs


(in situ detection) [18]. (genera) (family), rRNA . rRNA DNA-DNA . rRNA . Fox [19] Bacillus rRNA 99.5% DNA-DNA , 16S rRNA . Stackebrandt Goebel[20] 16S rRNA DNA-DNA . 16S rRNA DNA-DNA . 16s rRNA DNA-DNA 70% DNA (sequence identity) 97% [20]. 97% rRNA , , 16S rRNA [18]. 97% 16S rRNA DNA-DNA 60% DNA-DNA [20]. 16S rRNA Clinical and Laboratory Standards Institute (CLSI) [21]. CLSI % 99% 0.5-0.8% , 97% . rRNA rRNA rRNA 97% rRNA DNA-DNA [1]. Epsilonproteobacteria

16S rRNA (intraspecies) 4.5% [22,23]. . 1995 Clayton [24] Genbank rRNA . (intraspecies) 16S rRNA . (variability) , (strain-to-strain) , . . Jaspers Overmann [25] 16S rRNA , (ecophysiologies) . (chronometer) . , ATPase beta , elongation factor Tu, chaperonin, RNA polymerases - superoxide dismutase . 16S rRNA . [1]. 2) (phenotypic method): (subspecies), (genera) (family) , (phylogenetic tree) . (hierarchical line) [3,15]. (group) . . , , . (, , , , Gram ) (, , ) . ,


pH , (salt) , , , , . . . (1) (numerical) : (computer-assisted numerical comparison) . [26,27]. (matrices) (cluster analyses) . [1]. 3) (chemical method): . (1) (cellular fatty acid analysis): 300 . (bilayer) . (chain) (substituent groups) [28]. . methyl ester . (gas-liquid chromatography) . . . . (2) Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS): MALDI-TOF MS , , Alzheimer , , (biomarker) [29,30]. MALDI-TOF MS

(matrix) . . (flight tube) (mass/charge, m/z) . [31]. (desorb) , , (1-300 kDa) MALDI-TOF MS (biomolecules) . . . . MALDI-TOF MS .

3.

. . . 1) : . . (affiliation) . 16S rRNA . rRNA (MicroSeq500 16S rDNA Bacterial Sequencing Kit ) . 16S rRNA 5- (Escherichia coli 60 110 ) [17]. rRNA DNA-DNA (proposal)[32] (Whole genome based analyses) . 16S rRNA (genera) . rRNA


. (strain-to-strain) (interoperon) . 16S rRNA , , 16S rRNA 97% . (partial) rRNA , [7,17]. 16S rRNA (gold standard) [33]. 2) : rRNA , -(whole-cell) , ribotyping , MALDI-TOF MS, , microarray, , , (miniaturized series) . . . ( 16S rRNA ), . , , .

. Cowan ( ) (2 )

, . Cowan . . DNA-DNA 16S rRNA . . [1].

2009 .

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: , 501-717, 588 Tel: 062-220-3272, Fax: 062-232-2063E-mail: [email protected]

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