rpoB-PCR amplified gene and temporal temperature gradient gel electrophoresis: A rapid tool to analyse bacterial strains representative of cold-smoked salmon microflora

Letters in Applied Microbiology

Volumn 38, Issue 2, 2004, Pages 130-134

  Giacomazzi, S ^a   Leroi, F ^a   L'Henaff, C ^b   Joffraud, J J ^a  

^a IFREMER   (France)

^b LUNAM UNIVERSITÉ   (France)

Author keywords

Cold smoked salmon flora; Nested PCR; rpoB; TTGE

Indexed keywords

BACTERIA; BIODIVERSITY; ELECTROPHORESIS; POLYMERASE CHAIN REACTION; THERMAL GRADIENTS;

COLD-SMOKED SALMON; COLD-SMOKED SALMON FLORA; GEL ELECTROPHORESIS TECHNIQUE; NESTED PCR; NESTED POLYMERASE CHAIN REACTION; PURE CULTURE; REFERENCE STRAINS; RPOB; TEMPORAL TEMPERATURE GRADIENT GEL ELECTROPHORESIS; TTGE;

GENES;

BIOLOGICAL MARKER; DNA; PRIMER DNA; RNA POLYMERASE BETA SUBUNIT;

FOOD SAFETY; MICROBIOLOGY; POLYMERASE CHAIN REACTION;

ARTICLE; BACTERIAL FLORA; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; DNA DETERMINATION; EVALUATION; GEL ELECTROPHORESIS; GENE AMPLIFICATION; MICROBIAL DIVERSITY; NONHUMAN; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; SALMON; SEPARATION TECHNIQUE; TECHNIQUE; TEMPERATURE DEPENDENCE;

BACTERIA (MICROORGANISMS);

EID: 1242337998     PISSN: 02668254     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1472-765X.2003.01463.x     Document Type: Article

References (28)

1. Amann, R.I. (1995) In situ identification of micro-organisms by whole cell hybridization with rRNA-targeted nucleic acid probes. In Molecular Microbial Ecology Manual. pp. 1-15. Kluver Academic Publishers.
2. Amikam, D., Razin, S. and Glaser, G. (1982) Ribosomal RNA genes in Mycoplasma. Nucleic Acids Research 10, 4215-4222.
3. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. and Struhl, K. (ed.) (2002) Current Protocols in Molecular Biology, vol. 1. New York: John Wiley and Sons.
4. Cambon-Bonavita, M.A., Lesongeur, F., Menoux, S., Lebourg, A. and Barbier, G. (2001) Microbial diversity in smoked salmon examined by a culture-independent molecular approach - a preliminary study. International Journal of Food Microbiology 70, 179-187.
5. Cocolin, L., Manzano, M., Cantoni, C. and Comi, G. (2000) Development of a rapid method for the identification of Lactobacillus spp. isolated from naturally fermented italian sausages using a polymerase chain reaction-temperature gradient gel electophoresis. Letters in Applied Microbiology 30, 126-129.
6. Dahllöf, I., Baillie, H. and Kjelleberg, S. (2000) rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Applied and Environmental Microbiology 66, 3376-3380.
7. De Man, J.C., Rogosa, M. and Sharpe, M.E. (1960) A medium for the cultivation of Lactobacilli. Journal of Applied Bacteriology 23, 130-135.
8. Farrely, V., Rainey, F.A. and Stackebrandt, E. (1995) Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Applied and Environmental Microbiology 61, 2798-2801.
9. Fogel, G.B., Collins, C.R., Li, J. and Brunk, C.F. (1999) Prokaryotic genome size and SSU rDNA copy number: estimation of microbial relative abundance from a mixed population. Microbial Ecology 38, 93-113.
10. Giacomazzi, S. (2002) Mise au point et validation de techniques d'évaluation des communautés microbiennes dans les milieux complexes de type sols. PhD Thesis. Université de Technologie de Compiègne, Compiègne, France.
11. Giraffa, G. and Neviani, E. (2001) DNA-based, culture-independent strategies for evaluating microbial communities in food-associated ecosystems. International Journal of Food Microbiology 67, 19-34.
12. Gravelat, F.N. (2002) Mise en oeuvre de processus bactériens de déshalogénation et de dégradation des polychlorobiphényles pour la bioremédiation d'un sol pollué. Utilisation du polymorphisme des gènes rpoB et bphC pour le suivi des souches bactériennes dans le sol. PhD Thesis. Université de Technologie de Compiègne, Compiègne, France.
13. Jarvis, E.D., Widom, R.L., LaFauci, G., Setoguchi, Y., Richter, I.R. and Rudner, R. (1988) Chromosomal organization of rRNA operons in Bacillus subtilis. Genetics 120, 625-635.
14. Jorgensen, B.R. and Huss, H.H. (1989) Growth and activity of Shewanella putrefaciens isolated from spoiling fish. International Journal of Food Microbiology 9, 51-62.
15. Leroi, F., Joffraud, J.J., Chevalier, F. and Cardinal, M. (1998) Study of the microbial ecology of cold smocked salmon during storage at 8°C. International Journal of Food Microbiology 39, 111-121.
16. Leroi, F., Joffraud, J.J., Chevalier, F. and Cardinal, M. (2001) Research of quality indices for cold-smoked salmon using a stepwise multiple regression of microbiological counts and physio-chemical parameters. Journal of Applied Microbiology 90, 578-587.
17. Niemi, R.M., Heiskanen, I., Wallenius, K. and Lindström, K. (2001) Extraction and purification of DNA in rhizosphere soil samples for PCR-DGGE analysis of bacterial consortia. Journal of Microbiological Methods 45, 155-165.
18. Ogier, J.-C., Son, O., Gruss, A., Tailliez, P. and Delacroix-Buchet, A. (2002) Identification of the bacterial microflora in dairy products by temporal temperature gradient gel electrophoresis. Applied and Environmental Microbiology 68, 3691-3701.
19. Paludan-Müller, C., Dalgaard, P., Huss, H.H. and Gram, L. (1998) Evaluation of the role of Carnobacterium piscicola in spoilage of vacuum and modified atmosphere-packed-smoked salmon stored at 5°C. International Journal of Food Microbiology 39, 155-166.
20. Peixoto, R.S., da Costa Coutinho, H.L., Rumjanek, N.G., Macrae, A. and Rosado, A.S. (2002) Use of rpoB and 16SrRNA genes to analyse bacterial diversity of a tropical soil using PCR and DGGE. Letters in Applied Microbiology 32, 316-320 (Abstract).
21. Rosado, A.S., Duarte, G.F., Seldin, L. and Van Elsas, J.D. (1998) Genetic diversity of nifH gene sequences in Paenibacillus azotofixans strains and soil samples analysed by denaturing gradient gel electrophoresis of PCR-amplified gene fragments. Applied and Environmental Microbiology 64, 2770-2779 (Abstract).
22. Sheffield, V.C., Cox, D.R., Lerman, L.S. and Myers, R.M. (1989) Attachment of a 40-base-pair G+C-rich sequence (GC clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proceedings of the National Academy of Sciences of the USA 86, 232-236.
23. Stohr, V., Joffraud, J.J., Cardinal, M. and Leroi, F. (2001) Spoilage potential and sensory profile associated with bacteria isolated from cold smoked salmon. Food Research International 34, 797-806.
24. Truelstrup Hansen, L. (1995) Quality of chilled vacuum-packed cold-smoked salmon. PhD Thesis. Danish Institute for Fisheries Research and The Royal Veterinary and Agricultural University of Copenhagen, Denmark.
25. Truelstrup Hansen, L., Drewes Ronved, S. and Huss, H.H. (1998) Microbiological quality and shelf life of cold-smoked salmon from three different processing plants. Food Microbiology 15, 137-150.
26. Vasquez, A., Ahrné, S., Pettersson, B. and Molin, G. (2001) Temporal temperature gradient gel electrophoresis (TTGE) as a tool for identification of Lactobacillus casei, Lactobacillus paracasei, Lactobacillus zeae and Lactobacillus rhamnosus. Letters in Applied Microbiology 32, 215-219 (Abstract).
27. Wang, G.C. and Wang, Y. (1997) Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes. Applied and Environmental Microbiology 63, 4645-4650.
28. Young, M. and Cole, S.T. (1993) Clostridium. In Bacillus subtilis and Other Gram-positive Organisms ed. Sonenshein, J.A.H.A.L. and Losick, R. pp. 35-52. Washington, DC: American Society for Microbiology.