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. 2013 Sep 24;5:27. doi: 10.1186/1757-4749-5-27

Table 1.

Experiment duration and detection level for each method

Method
 Duration (ha)
 Time in total (h)
 Detection at the level of…
 Quantification
    Culture-dependent Culture-independentb Genus Species Subspecies  
Morphology
 *c
 ~ 48
 / d
 -e
 -
 -
 -
FTIR
 * + 1 h (analyzation)
 ~ 49
 /
 +f
 +
 -
 -
MALDI-TOF MS
 * + 1 h (analyzation)
 ~ 49
 /
 +
 +
 +
 -
API 50 CHL
 * + 48 h (incubation)
 ~ 96
 /
 +
 +
 -
 -
BIOLOG
 * + 25 h (24 h incubation of AN MicroPlateTM + 1 h analyzation)
 ~ 72
 /
 +
 +
 -
 -
16S/23S rRNA PCR + sequencing
 * + 31 h (4 h DNA isolation + 3 h PCR + 24 h sequencing)
 ~ 79
 ~ 31
 +
 +
 -
 -
PCR-DGGE
 * + 7 h (4 h DNA isolation + 3 h PCR + electrophoresis)
 ~ 55
 ~ 7
 +
 +
 -
 (+)g
RAPD
 * + 7 h (4 h DNA isolation + 3 h PCR + electrophoresis)
 ~ 55
 ~ 7
 +
 +
 +
 -
SSCP
 * + 7 h (4 h DNA isolation + 3 h PCR + electrophoresis)
 ~ 55
 ~ 7
 +
 +
 -
 -
MLST
 * + 31 h (4 h DNA isolation + 3 h qPCR + 24 h sequencing)
 ~ 79
 ~ 31
 +
 +
 +
 -
qPCR
 * + 7 h (4 h DNA isolation + 3 h qPCR)
 ~ 55
 ~ 7
 +
 +
 -
 +
SSR
 * + 7 h (4 h DNA isolation + 3 h PCR + electrophoresis)
 ~ 55
 ~ 7
 +
 +
 +
 -
WGS * + 4 h DNA isolation + 36 h Sequencing, annotation, etc.) ~ 88 ~ 40 + + + -

a h, hour(s).

b duration exclusive cultivation of the strains (48 h).

c *, isolation of the strains by plating on different media (MRS broth [Roth, Germany [14]], LBS agar [Becton Dickinson, USA [15]], COL and CHOC plates [Sarstedt, Germany]).

d /, identification of the strains not possible by working culture-independent.

e -, detection at the level of… is not possible.

f +, detection at the level of… is possible.

g (+), a limited quantification is possible using PCR-DGGE.