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Molecular Identification of Lactobacillus Hilgardii and Genetic Relatedness with Lactobacillus Brevis

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Molecular Identification of Lactobacillus Hilgardii and Genetic Relatedness with Lactobacillus Brevis International Journal of Systematic Bacteriology (1 999). 49, 1075-1 081 Printed in Great Britain Molecular identification of Lactobacillus hilgardii and genetic relatedness with Lactobacillus brevis Daniele Sohier, Joana Coulon and Aline Lonvaud-Funel Author for correspondence: Aline Lonvaud-Funel. Tel: +33 5 56 84 64 66. Fax: +33 5 56 84 64 68. e-mail : aline. lonvaud @ oenologie. u- bordeaux2.fr FacultC d'CEnologie-Unite Conventional phenotypic methods lead to misidentification of the lactic acid associCe INRA-U n iversite bacteria Lactobacillushilgardii and Lactobacillusbrevis. Random amplified Victor Segalen-Bordeaux 11, 351 Cows de la LibCration, polymorphic DNA (RAPD) and repetitive element PCR (REP-PCR) techniques 33405 Talence CCdex, were developed for a molecular study of these two species. The taxonomic France relationships were confirmed by analysis of the ribosomal operon. Amplified DNA fragments were chosen to isolate L. hilgardii-specific probes. In addition to rapid molecular methods for identification of L. hilgardii, these results convincingly proved that some strains first identified as L. brevis must be reclassified as L. hilgardii. The data clearly showed that these molecular methods are more efficient than phenotypic or biochemicalstudies for bacterial identification at the species level. I Keywords : Lactobacillus hilgardii, Lactobacillus brevis, RAPD, REP-PCR INTRODUCTION phenotypically close (Kandler & Weiss, 1986), they differ by their ability to ferment arabinose: L. brevis Lactic acid bacteria are responsible for malolactic can use this carbohydrate while L. hilgardii cannot. fermentation, an important step in winemaking et al., et al., In the present study, we intended to discriminate L. (Lafon-Lafourcade 1983; Renault 1988). hilgardii L. brevis However, some of them induce spoilage (Lonvaud- and by using molecular methods Funel & Joyeux, 1982; Lonvaud-Funel et al., 1990). based on DNA amplification. Genomic fingerprinting Therefore, specific detection and identification are of both species using random amplified polymorphic useful for quality control. Precision and reliability of DNA (RAPD) amplification on the one hand, and the phenotypical descriptions are not sufficient repetitive element PCR (REP-PCR) on the other, was enough, and some misidentifications occur (Kandler & assayed. Single primers corresponding to an arbitrary & sequence can be used to amplify genomic DNA Weiss, 1986; Lafon-Lafourcade Joyeux, 1979). sequences in order to generate genomic patterns Molecular approaches offer new opportunities to et al., characterize micro-organisms. Lonvaud-Funel et al. (William 1990). Depending on the type of primer used and on the conditions of the reaction, random (1990, 1991) describe the identification of lactic acid amplification of bacterial genomes generate suitable bacteria during vinification and wine storage by DNA-DNA hybridization. Genomic DNA of the fingerprints for characterization at the genus, species, or particular strain level (Fani et al., 1993). The REP- strain to be identified is hybridized with total genomic et al. DNA probes extracted from reference strains. How- PCR developed by Versalovic (199 1) is currently ever a problem arose because of cross-hybridization used to estimate relative degrees of similarity between L. brevis different isolates and to generate species-specific finger- between some strains isolated from wines, et al., & Lactobacillus brevis ATCC 11577 and Lactobacillus prints (Gilson 1991; Lupski Weinsthock, 1992 ; Rodriguez-Barradas, 1995). This method uses a hilgardii ATCC 8290T(Vescovo et al., 1979; Lonvaud- Funel et al., 1991). Although these two species are short, highly conserved extragenic repetitive sequence named the Repetitive Extragenic Palindromic (REP) consensus sequence. This sequence is present through- Abbreviations: RAPD, random amplified polymorphic DNA; REP-PCR, out the eubacterial kingdom, and it has been repetitive element PCR. demonstrated by Gilson et al. (1991) that its location The GenBank accession number for the 1.Rep probe sequence reported in is conserved in a given bacterial species. Thus this paper is AJ006299. the distribution of these dispersed repetitive DNA 00927 0 1999 IUMS 1075 D. Sohier, J. Coulon & A. Lonvaud-Funel sequences is supposed to be different through L. Table I. Bacterial strains used hilgardii and L. brevis genomes, in order to generate ....................................................................................... .. .......... ..... ......... ......... ...... ............... species-specific pat terns. ATCC, American Type Culture Collection; IOEB, Institut d'anologie de Bordeaux; DSM, Deutsche Sammlung von Molecular hybridization methods using specific DNA Mikroorganismen und Zellkulturen ; T, Type strain. probes are also useful for the detection and identi- fication of micro-organisms. They are particulary Species and strain Source efficient when used in colony hybridization to study ~ mixed populations. According to the strategy devel- Lactobacillus hilgardii oped by Fani et al. (1993), the amplification products ATCC 8290T Grape specific to L. hilgardii were purified and used as species- IOEB 7701 Grape specific DNA probes. IOEB 7902 Fermenting white grape must The rRNA-based studies represent an alternative to IOEB 720 Wine establish or to confirm relationships between strains IOEB 8408 Sweet white wine and species (Delong et al., 1989; Barry et al., 1990; IOEB 8510 Red wine Amann et al., 1996). Such investigations were per- IOEB 9101 Muscat formed by comparing the 165 rDNA genes of repre- IOEB 9102 Maury sentatives of the two species. IOEB 9202 Port IOEB 9515 Rivesaltes METHODS IOEB 95 18 Floc de Gascogne IOEB 9519 Muscat Bacterial strains and growth conditions. The strains used in this study were obtained from ATCC (American Type IOEB 9644 Sweet white wine Culture Collection) and the IOEB (Institut d'CEnologie de IOEB 9648 Sweet white wine Bordeaux) collection (Table 1). They were cultured at 25 "C Lac tobac illus bre vis in MRS medium (supplier : Prolabo except where indicated) : ATCC 14869T Human faeces 4 g yeast extract 1-1 (Difco); 8 g beef extract 1-1 (Difco); ATCC 11577 Cheese contamination 10 g bactopeptone 1-1 (Difco); 20 g glucose 1-l; 2 g Tris ATCC 367 sodium citrate 1-'; 5 g sodium acetate 1-l; 2 g KH,PO, 1-l; DSM 20556 Green olives 0-2 g MgSO, .7H,O 1-' ; 0.05 g MnSO, .H,O 1-1 ; Tween 80, IOEB 7702 Grape 1 ml; malic acid to adjust pH to 5. Carbohydrate assimi- IOEB 7903 Fermenting white grape must lations were established by API 50 test (bioM6rieux) for each IOEB 8404 White wine strain at the initiation and during the work to avoid any doubt due to possible contamination. IOEB 8407 Sweet wine IOEB 851 1 Red wine Total genomic DNA extraction. DNA was extracted ac- IOEB 8907 Red wine cording to a slightly modified version of the method described by Gasson & Davies (1980). Cells from 10ml IOEB 9112 Fermenting white grape must cultures were collected, washed and treated with lysozyme IOEB 9647 Fermenting white grape must (5 mg ml-l final concentration) for 15 min at 37 "C. The IOEB 9649 Fermenting white grape must protoplasts were lysed with 20% SDS for 15 min. After addition of NaCl (1 M final concentration), the cell debris were precipitated for 1 h at 4 "C and eliminated by centri- fugation for 20 min at 10000 g. The sample was emulsified were done for each strain in order to evaluate the repro- with an equal volume phenol/chloroform/isoamyl alcohol ducibility of the results. Blanks without genomic DNA were (25: 24: 1, by vol.) and centrifuged for 15 min at 10000 g. used as control for each primer. The upper phase was emulsified with a volume of chloro- Isolation, cloning and sequencing of amplified DNAs. form/isoamyl alcohol (24: 1, v/v). The DNA was then Ten precipitated, dried and suspended in sterile water with microlitres of each amplification mixture was loaded on a RNase (10 mg ml-l). 1 YO (w/v) agarose (Eurobio) gel with TBE electrophoresis buffer (89 mM boric acid, 89 mM Tris, 2mM EDTA) In order to evaluate DNA concentration, an aliquot of the pH 8.0) containing 0.2 mg ethidium bromide ml-l and sample was run in an agarose gel electrophoresis with electrophoresed at 100 V for 30 min. Gels were visualized at ethidium bromide. The fluorescence was then compared 312 nm with a UV transilluminator. DNA fragments were with amounts of standard DNA. extracted from agarose gels using the GenElute Supelco kit Primers and DNA amplification conditions. Single-stranded (Boehringer Mannheim). oligonucleotides were synthesized by Genset (Paris, France) Amplified DNA fragments from the L. hilgardii type strain (Table 2). Amplification reactions were performed in a 50 1.11 I1 KS ( -) volume containing 50 ng total genomic DNA, 10-l' M each were cloned in pBluescript + / vector (Stratagene). primer, 0-2 mM dNTPs, 1.25 U Taq polymerase (Appligene The DNA fragments were extracted from agarose gels and inserted into EcoRV site of the plasmid. Escherichia coli XL- Oncor) with 5 pl 10 x PCR reaction buffer. The ampli- 1 fication reactions were performed in a Minicycler DNA Blue (Stratagene) was transformed by electroporation. Plasmid DNA from E. coli was extracted according to the thermal cycler (MJ Research). After a primary denaturation method of Birnboim & Doly (1979) at 95 "C for 12 min, Taq polymerase was added. Each amplification consisted of 30 cycles of 30 s denaturation at Amplicons or cloned DNAs were sequenced by ACT Gene 95 "C, 30 s at the annealing temperature of the primers
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