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for Lact. pentosus. In fact, identification at the species level Oligonucleotides and RAPD or PCR-specific
requires the back-up of a large database of rRNA sequences reaction
and, in the case of very closely related species, even rRNA
Oligonucleotides were synthesized by Eurogentec (Seraing,
sequence analysis may not be sufficient (Pot et al. 1993).
Belgium). The OPA3 primer (5?-AGTCAGCCAC-3?) was
DNA probes have also been described for the Lact. acidophilus
used in the RAPD reaction. The OPA3-EcoRI primer (5?-
group (Pot et al. 1993), Lact. helveticus (Pilloud and Mollet
CCGAATTCAGTCAGCCAC-3?) was used for re-ampli-
1990), Lact. curvatus (Petrick et al. 1988; Vogel et al. 1993)
fication of the 300 bp RAPD OPA3-DNA fragment for clon-
and Lact. delbrueckii (Delley et al. 1990) but PCR methods
ing. The PCR-specific reaction of Lact. plantarum was
are not usually employed to identify Lactobacillus species
performed using the specific primers LbPl1 (5?-
(Nakagawa et al. 1994). This method certainly would be of use
AATTGAGGCAGCTGGCCA-3?) and LbPl2 (5?-GAT-
in the food industry to identify rapidly and unambiguously
TACGGGAGTCCAAGC-3?) primers. The semi-universal
relevant strains in fermentation processes.
primers designated Lb1 (5?-AGAGTTTGATCATGGC
This study was undertaken to develop a quick method for
TCAG-3?) and Lb2 (5?-CGGTATTAGCATCTGT
the identification of Lact. plantarum and, in particular, to
TTCC-3?) in the present study were designed by Klijn
perfect a probe which could be used in hybridization pro-
(1993). These primers amplified a variable loop in 16S rRNA
cedures to specifically identify Lact. plantarum strains and
sequences of Lactobacillus species and were employed as a
to provide a PCR-specific reaction for quick detection or
positive control of PCR.
identification of Lact. plantarum.
Twenty-five ml of reaction mixture containing 50 ng of
template DNA, 5 pmol l⌧1 of a 10-mer primer OPA3 (in
RAPD reaction), or LbPl1/LbPl2 and Lb1/Lb2 primers (in
MATERIALS AND METHODS
PCR-specific reaction), 50 mmol l⌧1 of each dNTP and 0·8
U of Taq DNA polymerase (Appligene) with 2·5 ml of 10
Bacterial strains and growth conditions
PCR reaction buffer (Appligene) were overlaid with mineral
The bacterial strains employed in this study are listed in oil. The amplification reaction was performed in a DNA
Table 1. Strains were either derived from culture collections thermal cycler (Own E, Hybaid). The RAPD reaction was
or isolated from a wide variety of products. The Escherichia adapted from a method described by Meunier and Grimont
coli strain used for cloning was DH5a [F⌧supE44thi-1 recA1 (1993). Each sample was subjected to a primary denaturation
gyrA96 relA1 hsdR17 (rK⌧mK ) endA1 f80dlacZDM15 cycle at 95°C for 5 min and at 94°C for 30 s, 36°C for 1 min
D(lacZYA-argF)U169]. and 72°C for 1 min during 45 cycles. After a denaturation
Growth of LAB and Sporolactobacillus was performed in cycle at 95°C for 5 min, PCR specific amplification with
MRS broth (Difco) at 37°C under anaerobic conditions. Esch- LbPl1/LbPl2 plus Lb1/Lb2 primers was performed with
erichia coli was grown in YT medium (Gibco BRL) at 37°C template denaturation at 94°C for 30 s, primer annealing at
and Bacillus cereus was grown in PCA medium (Difco) at 54°C for 1 min and primer extension at 72°C for 1 min. In
30°C under aerobic conditions. both cases the reactions were terminated at 72°C for 10 min.
Bacterial DNA was extracted according to the method of Gel electrophoresis was carried out by applying 25 ml of sam-
Luchansky et al. (1991). After centrifugation and two washes ple to submerged horizontal 2% agarose (PCR) or 1·5%
in TE buffer (10 mmol l⌧1 Tris–HCl, pH 8·0; 1 mmol l⌧1 (RAPD) slab gel. Gels were run for 30 min at 50 V in TEB
EDTA), cells were resuspended in 1 ml of a lysis buffer electrophoresis buffer (89 mmol l⌧1 boric acid, 89 mmol l⌧1
(50 mmol l⌧1 Tris, pH 8·0; 1 mmol l⌧1 EDTA; 25% sac- Tris, 2 mmol l⌧1 EDTA) without cooling. A DNA molecular
charose) containing 40 mg ml⌧1 of mutanolysine (Sigma) and weight marker (superladder mid-1, Eurogentec) was used
20 mg ml⌧1 of lysozyme (Merck) and incubated for 45 min as standard. Gels were stained with ethidium bromide and
at 37°C. The reaction was stopped using 1 ml of EDTA visualized at 312 nm with a u.v. transilluminator (Fluo-Link,
(250 mmol l⌧1, pH 8·0) for 5 min. The samples were then Vilbert Lourmat, Marne-La-Vallée, France).
treated with 400 ml of 20% (w/v) SDS and 20 ml of a
20 mg ml⌧1 Proteinase K (Sigma) solution. The mixture was
Isolation of the amplified DNA
incubated at 65°C until it became clear and less viscous, and
then was treated by phenol–chloroform extraction. DNA was The 300 bp DNA fragment was extracted from the gel by
precipitated in ethanol and resuspended in 100 ml of TE electrolution. An oligonucleotide (EcoRI-OPA3) containing
buffer 10 ml of RNase (10 mg ml⌧1). the restriction enzyme site EcoRI was synthesized. The iso-
© 1997 The Society for Applied Bacteriology, Journal of Applied Microbiology 82, 783–790
D NA PR O BE AN D PC R F O R L AC T . P LA N TA RU M 785
© 1997 The Society for Applied Bacteriology, Journal of Applied Microbiology 82, 783–790
D NA PR O BE AN D PC R F O R L AC T . P LA N TA RU M 787
Table 1 (continued)
––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
—
PCR PCR
Dot-blot specific specific
membrane RAPD location location
Species and source location location (Fig. 4a) (Fig. 4b)
––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
—
Carnobacterium
piscicola DSM 20722 48 16 — —
piscicola DSM 20730T 65 — — —
divergens DSM 20623T 66 — — —
mobile DSM 4848T 67 — — —
Sporolactobacillus laevus IAM 12384T 68 — — —
Lactococcus lactis spp. lactis ATCC 11454T 16, 44 — — —
Pediococcus pentosaceus ATCC 33316T 70 — — —
Bacillus cereus* 69 — — —
Enterococcus faecalis CIP 76117T 71 — — —
Escherichia coli K 12* 72 — — —
––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
—
* This laboratory; † University of Seville, Spain; ATCC, American Type Culture Collection; DSM, Deutsche Sammlung von
Mikroorganismen; CNRZ, Centre National de Recherches Zootechniques; CIP, Collection Nationale de Cultures de Microorganismes de
l’Institut Pasteur, Paris, France; IAM, Institute of Applied Microbiology, University of Tokyo, Japan; F&B, Faculté d’'nologie de
Bordeaux; NCIMB, National Collection of Industrial and Marine Bacteria, Aberdeen, UK; NCFB, National Collection of Food Bacteria,
Reading, UK.
DISCUSSION
In modern taxonomy of bacteria, 16S and 23S rRNA
Fig. 2 Dot-blot hybridization with different Lactobacillus strains sequence analysis is a standard method for the investigation
and other genera; 300 ng of purified DNA were applied per spot of phylogenetic relationship (Fox et al. 1980) and can also
and processed as described in Materials and Methods. As probe: be used to design genus- or species-specific oligonucleotide
the a32P-labelled 300 bp fragment generated with OPA3 primer by probes for rapid identification and detection (Kingler and
RAPD. The strain membrane locations are listed in Table 1 Johnson 1988). Furthermore, this approach can be enhanced
© 1997 The Society for Applied Bacteriology, Journal of Applied Microbiology 82, 783–790
788 F . Q UE R E E T A L .
Fig. 4 (a) PCR-specific reaction with LbPl1/LbPl2 and Lb1/Lb2 primers. Lanes: 1 and 12, DNA molecular weight marker 100 bp;
2–11, Lactobacillus strains listed in Table 1. A 253 bp fragment amplified with LbPl1/LbPl2 primers was detected in lanes 6 and 9. The
194 bp fragment amplified with Lb1/Lb2 primers was present in every lane. (b) PCR-specific reaction with LbPl1/LbPl2 and Lb1/Lb2
primers. Lanes: PM, DNA molecular weight marker 100 bp; 0, negative control (without DNA); 1–10, Lact. plantarum strains as listed in
Table 1; 11–18, Lact. pentosus strains as listed in Table 1. A 253 bp fragment amplified with LbPl1/LbPl2 primers was detected in
lanes 1 and 10. The 194 bp fragment amplified with Lb1/Lb2 primers was present in every lane
by the application of the PCR which can be used to amplify et al. 1993; Richter et al. 1995) or plasmids (Cocconcelli et al.
rDNA sequences with specific primer sets. Nevertheless, the 1991) are rare. Specific DNA probes for Lact. curvatus, Lact.
difference in 16S rRNA sequences between Lact. plantarum helveticus and Lact. delbrueckii based on random screening of
and Lact. pentosus was small. Only three nucleotides were genomic DNA library and subsequent analysis of clones by
different when the 16S rRNA sequences of the two Lacto- dot-blot hybridization are described but the fragments have
bacillus species were compared (data not shown). The 23S not been sequenced (Petrick et al. 1988; Delley et al. 1990;
rRNA sequences for Lact. plantarum and Lact. pentosus are Pilloud and Mollet 1990).
not yet available. For closely related species it may be difficult We used random amplification of the DNA (RAPD) to
to generate specific oligonucleotide probes or specific primer develop a specific probe for Lact. plantarum. The RAPD
sets based on 16S rRNA. method reported here may be useful for the rapid devel-
DNA probes for lactobacilli other than those based on 16S opment of specific probes.
or 23S rRNA (Hertel et al. 1991; Castellanos et al. 1993; Pot The 300 bp fragment isolated from Lact. plantarum DSM
© 1997 The Society for Applied Bacteriology, Journal of Applied Microbiology 82, 783–790
D NA PR O BE AN D PC R F O R L AC T . P LA N TA RU M 789
20174 seemed to be conserved among the other strains of (1993) Ensiling characteristics of crab waste and wheat straw
Lact. plantarum species. A large number of strains belonging treated with different additives. Journal of Agricultural and Food
to the Lact. plantarum species isolated in this laboratory from Chemistry 41, 657–661.
a wide environmental diversity showed a high hybridization Birnboim, H.C. and Doly, J. (1979) A rapid alkaline extraction
procedure for screening recombinant plasmid DNA. Nucleic Acids
level with our specific DNA probe (data not shown).
Research 7, 1513–1523.
Weak hybridization signals were observed with two of the Bringel, F., Curk, M.C. and Hubert, J.C. (1995) Characterization
five Lact. pentosus strains tested. However, these signals could of Lactobacilli species by nucleic acid hybridizations. Proposition
be clearly differentiated from the stronger hybridization for a new species related with L. plantarum: L. paraplantarum.
obtained with the Lact. plantarum strains. A weak sequence Book of Abstracts. Lactic Acid Bacteria Conference, Cork, Ireland.
homology located in the 300 bp region may exist between Castellanos, I., Vékris, A. and Deschamps, A. (1993) Elaboration of
Lact. plantarum and Lact. pentosus. This probably reflects strain-specific probe for probiotic lactobacilli. FEMS Micro-
the close phylogenetic relationship of these two Lactobacillus biology Reviews 12, 153.
species. The determination of the 300 bp DNA probe speci- Cocconcelli, P.S., Triban, E., Basso, M. and Bottazzi, V. (1991)
ficity was confirmed by further results obtained with the Use of DNA probes in the study of silage colonization by Lacto-
primer set selected. In fact, a PCR-specific identification of bacillus and Pediococcus strains. Journal of Applied Bacteriology 71,
296–301.
Lact. plantarum is now available.
Collins, M.D., Rodrigues, U., Ash, C., Aguirre, M., Farrow, J.A.E.,
The use of the PCR for bacterial identification and detec- Martinez-Murcia, A. et al. (1991) Phylogenetic analysis of the
tion offers a considerable potential as a rapid method and genus Lactobacillus and related lactic acid bacteria as determined
combines speed, specificity, simplicity and sensitivity criteria. by reverse transcriptase sequencing of 16S rRNA. FEMS Micro-
It would be particularly useful when the species are pheno- biology Letters 77, 5–12.
typically closely related and hard to distinguish by con- Dellaglio, F., Botazzi, V. and Trovatelli, L.D. (1973) Deoxy-
ventional microbiological approaches. DNA probes have been ribonucleic acid homology and base composition in some thermo-
used in combination with PCR to detect specific bacteria. philic lactobacilli. Journal of General Microbiology 74, 289–297.
One of the applications of this technology is the identification Delley, M., Mollet, B. and Hottinger, H. (1990) DNA probe for
of human pathogens in food (Yamamoto and Harayama 1995). Lactobacillus delbrueckii. Applied and Environmental Microbiology
The probes were able to detect PCR products which were 56, 1967–1970.
Feinberg, A.P. and Vogelstein, B. (1984) A technique for radio-
not visible on the agarose gel (i.e. less that 1 ng of DNA)
labelling DNA restriction endonuclease fragments to high specific
(Wernars et al. 1991). PCR with Lbp1-Lbp2 primers or activity. Analytical Biochemistry 132, 6–13.
followed by specific probe hybridization may offer a very Fox, G.E., Stackebrandt, R.B., Hespell, J., Gibson, J., Maniloff,
sensitive detection of Lact. plantarum and should be a con- T.A., Dyer, R.S. et al. (1980) The phylogeny of prokaryotes.
siderable advantage in analysis of fermented food and silage. Science 209, 457–463.
Direct PCR on colonies selected with a toothpick can be Fujisawa, T., Benno, Y., Yaeshima, T. and Mitsuoka, T. (1992)
advantageous in terms of time and labour costs. Many col- Taxonomic study of the Lactobacillus acidophilus group, with
onies could be analysed in a short time and the average of recognition of Lactobacillus gallinarum sp. nov. and Lactobacillus
Lact. plantarum in the analysed product could be determined. johnsonii sp. nov. and synonymy of Lactobacillus acidophilus group
A DNA probe may also be used, for instance, to monitor the A3 (Johnson et al. 1980) with the type strain of Lactobacillus
amylovorus (Nakamura 1981). International Journal of Systematic
specific bacteria in food fermentations and silage processes
Bacteriology 32, 487–491.
by colony hybridization. Hertel, C., Ludwig, W., Obst, M., Vogel, R.F., Hammes, W.P.
In conclusion, a DNA probe and a PCR specific to Lact. and Schleifer, K.-H. (1991) 23S rRNA-targeted oligonucleotide
plantarum are described here. The use of this PCR, DNA probes for the rapid identification of meat Lactobacilli. Systematic
probe or PCR-DNA probe offers a rapid method for the and Applied Microbiology 14, 173–177.
identification and detection of Lact. plantarum and could be Johansson, M.L., Quednau, M., Molin, G. and Ahrné, S. (1995)
employed in analysis and monitoring of fermented foods and Randomly amplified polymorphic DNA (RAPD) for rapid typing
feeds where Lact. plantarum is usually implicated. of Lactobacillus strains. Letters in Applied Microbiology 21, 155–
159.
Johnson, J.L., Phelps, C.F., Cummins, C.S., London, J. and Gasser,
ACKNOWLEDGEMENT F. (1980) Taxonomy of the Lactobacillus acidophilus group. Inter-
national Journal of Systematic Bacteriology 30, 53–68.
This work was partly financed by the Conseil Régional de
Kingler, J.D. and Johnson, A.R. (1988) A rapid nucleic acid hybrid-
Bretagne, France, Project Britta No. 41 56 156. ization assay for Listeria in foods. Food Technology 42, 66–70.
Klijn, N., Weerkamp, A.H. and de Vos, W.M. (1991) Identification
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