Biomedical Engineering Reference
In-Depth Information
The species
S. cerevisiae
has been observed to show extensive pheno- and
genotypic intraspecies diversity (reviewed in [
214
]). Part of such strain diversity has
been traced by molecular analyses to genomic variability associated with Ty-element
insertion sites [
215
]. Ty elements belong to a group of eukaryotic transposable ele-
ments that are also called retrotransposons because of some similarities with retrovi-
ruses. Ty-elements are flanked by long terminal repeat (LTR) sequences, in turn
formed by repeated delta elements. Delta elements are also found in larger numbers
independently from LTR sequences and have been used to design and optimize
specific PCR primers to amplify the sequences between two delta elements in
S.
cerevisiae
, resulting in an effective strain-typing method for this species [
216,
217
] .
5.4.1.2
LAB
Although largely abandoned and replaced by molecular tools, characterization and
identification of sourdough LAB species by phenotypic methods is in some cases
still useful, or even mandatory when it concerns new species descriptions. The con-
ventional phenotypic approaches for identification of sourdough LAB species may
include physiological and chemotaxonomic tests and determination of major fer-
mentation pathways, carbohydrate utilization patterns, lactic acid configuration,
and peptidoglycan types. To determine carbohydrate patterns and enzymatic prop-
erties in a faster and more reproducible way, miniaturized biochemical test systems
such as the API system (Biomérieux, France) can be used for phenotypic character-
ization of sourdough LAB species [
23
]. However, it should be stressed that the
identifications obtained by comparison with commercial databases such as those
linked to API are only tentative and need verification with other taxonomic meth-
ods. A more advanced phenotypic identification approach is offered by chemotaxo-
nomic methods, which are based on the use of analytical methods to detect and
characterize one or several chemical cell components. Protein profiling by sodium
dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) has been used for
identification of LAB isolates recovered from Italian [
127
] and Greek [
72
] sour-
doughs. SDS-PAGE of cellular proteins generally offers sufficient discrimination of
LAB isolates at species level but may fail to discriminate between species in the
Lb.
acidophilus
group [
218
] and the
Lb. plantarum
group [
71
], both of which are promi-
nent members of sourdough ecosystems. Although not yet evaluated for sourdough
LAB, the use of mass spectrometry (MS) methods is probably the most powerful
phenotypic approach currently available for classification and identification of bac-
teria [
219
]. One of these methods, matrix-assisted laser desorption/ionization-time-
of-flight (MALDI-TOF) MS, allows one to measure peptides and other compounds
in the presence of salts and to analyze complex peptide mixtures, which makes it an
ideal method for measuring nonpurified extracts and intact bacterial cells. The
resulting MALDI-TOF MS spectra can be used to generate identification libraries
for simple and high-throughput identification of unknown bacterial isolates. De
Bruyne and co-workers [
220
] constructed such identification libraries for the LAB
genera
Leuconostoc
,
Fructobacillus,
and
Lactococcus
, and reported that 84% of the
