Identification of Lactobacillus alimentarius and Lactobacillus farciminis with 16S-23S rDNA intergenic spacer region polymorphism and PCR amplification using species-specific oligonucleotide

Journal of Applied Microbiology

Volumn 95, Issue 6, 2003, Pages 1207-1216

  Rachman, C N ^a   Kabadjova, P ^a   Prevost H ^a   Dousset, X ^a  

^a LUNAM UNIVERSITÉ   (France)

Author keywords

16S 23S rDNA; Intergenic spacer region; Lactobacillus alimentarius; Lactobacillus farciminis; Restriction fragment length polymorphism

Indexed keywords

BACILLI; CLONING; DNA SEQUENCES; ELECTROPHORESIS; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION;

16S-23S RDNA; INTERGENIC SPACER REGIONS; LACTOBACILLUS ALIMENTARIU; LACTOBACILLUS FARCIMINI; LACTOBACILLUS SPECIES; PCR AMPLIFICATION; RAPID IDENTIFICATION; RESTRICTION FRAGMENT LENGTH POLYMORPHISMS; SPECIES SPECIFICS; SPECIES-SPECIFIC PRIMERS;

ENZYMES;

BACTERIAL DNA; BACTERIAL RNA; DNA 16S; PRIMER DNA; RIBOSOMAL SPACER DNA; RIBOSOME DNA; RNA 16S; RNA 23S;

BACTERIUM; IDENTIFICATION METHOD; POLYMERASE CHAIN REACTION;

AGAR GEL ELECTROPHORESIS; ARTICLE; BACTERIUM IDENTIFICATION; CLASSIFICATION; GENETIC POLYMORPHISM; GENETICS; LACTOBACILLUS; LACTOBACILLUS ALIMENTARIUS; LACTOBACILLUS FARCIMINIS; LACTOBACILLUS PARAPLANTARUM; LACTOBACILLUS PLANTARUM; METHODOLOGY; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE;

BACTERIA (MICROORGANISMS); LACTOBACILLUS; LACTOBACILLUS ALIMENTARIUS; LACTOBACILLUS FARCIMINIS; LACTOBACILLUS PARAPLANTARUM; LACTOBACILLUS PLANTARUM; POSIBACTERIA;

EID: 0344304725     PISSN: 13645072     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2672.2003.02117.x     Document Type: Article

References (31)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI BLAST: a new generation of protein database search programs. Nucleic Acids Research 25, 3389-3402.
2. Amann, R.I., Ludwig, W. and Schleifer, K.H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology Review 59, 143-169.
3. Barry, T., Colleran, G., Glennon, M., Dunnican, L.K. and Gannon, F. (1991) The 16S/23S ribosomal spacer region as a target for DNA probes to identify eubacteria. PCR Methods and Applications 1, 51-56.
4. Berthier, F. and Ehrlich, S.D. (1998) Rapid species identification within two groups of closely related lactobacilli using PCR primers that target the 16S/23S rRNA spacer region. FEMS Microbiology Letters 161, 97-106.
5. Chagnaud, P., Machinis, K., Coutte, L.A., Marecat, A. and Mercenier, A. (2001) Rapid PCR-based procedure to identify lactic acid bacteria: application to six common Lactobacillus species. Journal of Microbiological Methods 44, 139-148.
6. Corsetti, A., Lavermicocca, P., Morea, M., Bazurri, F., Tosti, N. and Gobbetti, M. (2001) Phenotypic and molecular identification and clustering of lactic acid bacteria and yeasts from wheat (species Triticum durum and Triticum aestivum) sourdoughs of Southern Italy. International Journal of Food Microbiology 64, 95-104.
7. Gürtler, V. and Stanisich, V.A. (1996) New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142, 3-16.
8. Halami, P.M., Chandrashekar, A. and Nand, K. (2000) Lactobacillus farciminis MD, a newer strain with potential for bacteriocin and antibiotic assay. Letters of Applied Microbiology 30, 197-202.
9. Jensen, M.A., Webster, J.A. and Straus, N. (1993) Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Applied and Environmental Microbiology 59, 945-952.
10. Juven, B.J., Barefoot, S.F., Pierson, M.D., McCaskill, L.H. and Smith, B. (1998) Growth and survival of Listeria monocytogenes in vacuum-packaged ground beef with Lactobacillus alimentarius FloraCarn L-2. Journal of Food Protection 61, 551-556.
11. Kabadjova, P., Dousset, X., Le Cam, V., and Prévost, H. (2002) Differentiation of closely related Carnobacterium food isolates based on 16S-23S ribosomal DNA intergenic spacer region polymorphism. Applied and Environmental Microbiology 68, 5358-5366.
12. Krawiec, S. and Riley, M. (1990) Organization of the bacterial chromosome. Microbiology Review 54, 502-539.
13. Le Jeune, C. and Lonvaud-Funel, A. (1997) Sequence of DNA 16S/23S spacer region of Leuconostoc oenos (Oenococcus oeni): application to strain differentiation. Research in Microbiology 148, 79-86.
14. Lemay, M.J., Choquette, J., Delaquis, P.J., Claude, G. and Saucier, L. (2002) Antimicrobial effect of natural preservatives in a cooked and acidified chicken meat model. International Journal of Food Microbiology 78, 217-226.
15. Leroi, F., Joffraud, J.J., Chevalier, F. and Cardinal, M. (1998) A study of the microbial ecology of cold smoked salmon during storage at 8°C. International Journal of Food Microbiology 39, 111-121.
16. Lyhs, U., Korkeala, H., Vandamme, P. and Björkroth, J. (2001) Lactobacillus alimentarius: a specific spoilage organism in marinated herring. International Journal of Food Microbiology 64, 355-360.
17. Navarro, E., Simonet, P., Normand, P. and Bardin, R. (1992) Characterization of natural populations of Nitrobacter spp. using PCR/RFLP analysis of the ribosomal intergenic spacer. Archives of Microbiology 157, 107-115.
18. Nour, M. (1998) 16S-23S and 23S-5S intergenic spacer regions of lactobacilli: nucleotide sequence, secondary structure and comparative analysis. Research in Microbiology 149, 433-448.
19. Paludan-Müller, C., Madsen, M., Sophanodora, P., Gram, L. and Moller, P.L. (2002) Fermentation and microflora of plaa-som, a thai fermented fish product, prepared with different salt concentrations. International Journal of Food Microbiology 73, 61-70.
20. Reuter, G. (1983) Lactobacillus alimentarius sp. nov., nom rev. and Lactobacillus farciminis sp. nov., nom rev. Systematic and Applied Microbiology 4, 277-279.
21. Ruiz, A., Poblet, M., Mas, A. and Guillamon, J.M. (2000) Identification of acetic acid bacteria by RFLP of PCR-amplified 16S rDNA and 16S-23S rDNA intergenic spacer. International Journal of Evolutionary Microbiology 50, 1981-1987.
22. Sambrook, J. and Russell, D.W. (2001) Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
23. Sanger, F., Nicklen, S. and Coulson, A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences USA 74, 5463-5467.
24. Song, Y.L., Kato, N., Liu, C., Matsumiya, Y., Kato, H. and Watanabe, K. (2000) Rapid identification of 11 human intestinal Lactobacillus species by multiplex PCR assays using group-and species-specific primers derived from the 16S-23S rRNA intergenic spacer region and its flanking 23S rRNA. FEMS Microbiology Letters 187, 167-173.
25. Tanasupawat, S., Okada, S. and Komagata, K. (1998) Lactic acid bacteria found in fermented fish in Thailand. Journal of Genetic and Applied Microbiology 44, 193-200.
26. Tanasupawat, S., Thongsanit, J., Okada, S. and Komagata, K. (2002) Lactic acid bacteria isolated from soy sauce mash in Thailand. Journal of Genetic and Applied Microbiology 48, 201-209.
27. Tannock, G.W., Tilsala-Timisjarvi, A., Rodtong, S., Ng, J., Munro, K. and Alatossava, T. (1999) Identification of Lactobacillus isolates from the gastrointestinal tract, silage and yoghurt by 16S-23S rRNA gene intergenic spacer region sequence comparison. Applied and Environmental Microbiology 65, 4264-4267.
28. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673-4680.
29. Tilsala-Timisjärvi, A. and Alatossava, T. (1997) Development of oligonucleotide primers from the 16S-23S rRNA intergenic sequences for identifying different dairy and probiotic lactic acid bacteria. International Journal of Food Microbiology 35, 49-56.
30. Trcek, J. and Teuber, M. (2002) Genetic and restriction analysis of the 16S-23S rDNA internal transcribed spacer regions of acetic acid bacteria. FEMS Microbiology Letters 208, 69-75.
31. Tudor, J.J., Marri, L., Piggot, P.J. and Daneo-Moore, L. (1990) Size of the Streptococcus mutans GS-5 chromosome as determined by pulsed-field gel electrophoresis. Infection and Immunity 58, 838-840.