Korean J Clin Microbiol Vol. 15, No.

3, September, 2012
http://dx.doi.org/10.5145/KJCM.2012.15.3.79

Basic Concepts of Bacterial Taxonomy

Young 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, bacterial classification and identification were performed
based on the morphology and the biochemical data
of the bacteria. In newer theories, or so-called natural concepts, the relationships between bacteria are
based on the overall similarities of both the phenotypic and genotypic characteristics. The polyphasic
taxonomy, or current taxonomy, describes the integration 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 differentiate 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

[2].
.

(systematics) (classifi-

cation), (nomenclature) (identification)

(similarity) (taxo-

nomic group) .

1) :

[1].

.
,

1.

.


. (numerical)

(chemotaxonomic) (genotypic)

1987 Ad Hoc

(phenetics)

Received 11 February, 2012, Revised 14 March, 2012

Accepted 25 March, 2012
Correspondence: 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) sjbjang@chosun.ac.kr

[3]. - DNADNA(whole-genome DNA-DNA hybridization)

.

79

80

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

DNA-DNA 70% Tm

tussis B. parapertussis B. bronchiseptica DNA-

5oC ( ) . Tm

DNA 80%

(hybrid)

Tm . Tm

[9]. Acidovorax

(homologous hybrid) (heterologous hybrid)

(genera) DNA-DNA

Tm( ) [4].

40%

DNA-DNA

[10].

DNA-DNA

Wayne DNA-DNA

(DNA-DNA hybridization)

DNA-DNA

[4].

(genomic species) genomo-

var [5].

2) (polyphasic) : Colwell[6]

DNA-

(polyphasic taxonomy) , ,

DNA , 16S rRNA

(chemotaxonomic),

(genus) (family), (order)

(ranks) .

DNA

DNA (base)

(genome size), , ,

16S rRNA

. rRNA

(fraction)
[7].

3) : (prokaryotic)

(mycolic

acid), , , (sugars), polyamines, qui-

, , ,

nones, (, ,

[1].

[11,12].

rRNA (signature features)

. ATPase beta subunit, elongation factor Tu,

chaperonin, , RNA polymerase

tRNA

, ,

[7,8].

, ,

. DNA-DNA

(nucleotide signature composition) ,

(metabolic pathway reaction content anal-

yses) . (multilo-

. Bordetella per-

cus sequence analysis, MLSA)

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

.
MLSA (multilocus sequence typing, MLST) 4-10
(housekeeping gene) DNA
. PCR
.

81

backbone) 16S rRNA

(intraspecies) [1].
2.
, ,

MLST

, MLSA

(DNA RNA)

, (chemo-

[13].

taxonomic markers)

MLST

, MLSA

(genera)

, .

. MLST

1)

(1) DNA-DNA : DNA-DNA

(allelic profiles) .

. DNA-DNA (DNA-DNA hybridization)

DNA

. MLST

. DNA

(downstream analyses)

. MLSA DNA

. MLSA

[13] (Fig. 1).

DNA

DNA .

16S rRNA

()(heteroduplex) (thermal stabil-

. (phylogenetic

ity) (genetic diverge-

Fig. 1. Schematic diagram showing

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

82

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

nce) [14]. ,

DNA DNA .

[15].

DNA

DNA (hybrid double-stranded DNA) .

DNA-DNA

. DNA

. , DNA-DNA ,

DNA-DNA , DNA-DNA

. DNA-DNA

DNA column

. column

DNA-DNA

(cut off)

. DNA column

. DNA-DNA

(homologous hybrid) (heterologous hybrid)

DNA-DNA .

Tm Tm DNA

(2) rRNA : rRNA

DNA

(target) .

[14] (Fig. 2).

16S 23S rRNA

PCR

(direct sequencing) .

[16,17].

DNA-DNA

(conserved elements)

, ,

. rRNA motifs

Fig. 2. Schematic diagram showing DNA-DNA hybridization procedure. (A) The DNA-DNA hybridization step. The DNA of two species of
bacteria 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.

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

83

16S rRNA (intraspecies)

(in

4.5% [22,23].

situ detection)
[18].

. 1995 Clayton [24]

(genera) (family),

Genbank rRNA

rRNA

. rRNA

(intraspecies) 16S rRNA

DNA-DNA

(variability)

rRNA .

, (strain-to-strain)

Fox [19] Bacillus

rRNA 99.5% DNA-DNA

, 16S rRNA

Jaspers Overmann [25]

.
Stackebrandt Goebel[20]
16S rRNA DNA-DNA

16S rRNA ,
(ecophysiologies)
.

. 16S rRNA

DNA-DNA

(chronometer)

. 16s rRNA

. ,

DNA-DNA 70% DNA

ATPase beta , elongation factor Tu, chaperonin, RNA

(sequence identity)

polymerases - superoxide dismutase

97% [20]. 97%

rRNA ,

16S rRNA

16S rRNA .

[18]. 97%

16S rRNA

[1].

DNA-DNA 60%
DNA-DNA [20].

2) (phenotypic method):
(subspecies), (genera) (family)

(phylogenetic tree)

16S rRNA

Clinical and Laboratory Standards Institute (CLSI)

(hierarchical line)

[21]. CLSI %

[3,15].

99% 0.5-0.8%

(group)

, 97%

rRNA rRNA

rRNA

, ,

97%

rRNA DNA-DNA

. (, , ,

[1].
Epsilonproteobacteria

, Gram ) (, , )
. ,

84

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

pH , (salt) ,

(matrix) .

, ,

(flight tube)

(mass/charge, m/z)

[31].

(1) (numerical) :

(desorb) , ,

(computer-assisted numerical comparison)

(1-300 kDa) MALDI-TOF MS

(biomolecules)

[26,27].

(matrices) (cluster analyses)

MALDI-TOF MS

[1].
3) (chemical method):

.

3.
.

(1) (cellular fatty acid analysis): 300

(bilayer)

. (chain)

1) :

(substituent groups)

[28].

. methyl

ester .

(affiliation) .

(gas-liquid chromatography)

16S rRNA

. rRNA

(MicroSeq500 16S

rDNA Bacterial Sequencing Kit ) . 16S rRNA

5- (Escherichia coli

60 110 )

[17].

rRNA

(2) Matrix-assisted laser desorption ionization time-of-flight

DNA-DNA

mass spectrometry (MALDI-TOF MS): MALDI-TOF MS

(proposal)[32]

(Whole genome based analyses)

, Alzheimer , ,

(biomarker)

16S rRNA (genera)

[29,30]. MALDI-TOF MS

. rRNA

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

85

, . Cowan

(strain-to-strain)
(interoperon) .

DNA-DNA

16S rRNA

16S rRNA

, 16S rRNA

97%

[1].

(partial)
rRNA

,

[7,17]. 16S rRNA

2009
.

(gold standard)

[33].
2) : rRNA , -(whole-cell)
, ribotyping , MALDI-TOF MS,
, microarray, ,
, (miniaturized
series)
.

.

.
(
16S rRNA ),

.

,
, .

. Cowan (
) (2
)

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

==

1, 2
1, 2
(classification), (nomenclature) (identification).
, .
, .
(polyphasic taxonomy) , ,
. 16s rRNA
. 16s rRNA

. [ 2012;15:79-87]
: , 501-717, 588

Tel: 062-220-3272, Fax: 062-232-2063
E-mail: sjbjang@chosun.ac.kr

87