rpoB-PCR amplified gene and temporal temperature gradient gel electrophoresis: a rapid tool to analyse bacterial strains representative of cold-smoked salmon microflora.
OBJECTIVE
To evaluate rpoB gene as a biomarker of microbial biodiversity associated to cold-smoked salmon by a novel nested-polymerase chain reaction/temporal temperature gradient gel electrophoresis (PCR/TTGE) technique applied on pure cultures of reference strains.


RESULTS
DNA obtained from pure cultures of reference strains was used in a succession of a first PCR amplification of rpoB fragment with degenerated nonclamped primers and a nested-PCR with nondegenerated clamped primers. PCR products were then applied on a TTGE gel in order to analyse strains profile. High quantity of nested-PCR products were obtained for each tested strain and TTGE profiles showed a good separation between the different reference bacteria and an easy way to associate one band to one species.


CONCLUSIONS
The nested-PCR/TTGE technique used in this study is a promising way of investigating bacterial community structure of cold-smoked salmon or other food matrix.


CONCLUSIONS
Because of its single copy state leading to single band profiles in TTGE, rpoB constitute a good potential molecular marker for further development of cold-smoked salmon biodiversity analysis.
Giacomazzi
S
S
Laboratoire de Génie Alimentaire, IFREMER, Rue de l'île d'Yeu, Nantes Cedex, France.
Leroi
F
F
L'Henaff
C
C
Joffraud
J-J
JJ
D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000302:isolation & purification*; D044822:Biodiversity; D004269:DNA, Bacterial / Q000032:analysis / Q000302:isolation & purification; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods; D005516:Food Microbiology; D005798:Genes, Bacterial; D009691:Nucleic Acid Denaturation; D016133:Polymerase Chain Reaction; D012474:Salmon / Q000382:microbiology*; D013696:Temperature
D004269:DNA, Bacterial; D012321:DNA-Directed RNA Polymerases; C105078:RNA polymerase beta subunit