A rapid PCR procedure for the specific identification of Lactobacillus sanfranciscensis, based on the 16S-23S intergenic spacer regions.
OBJECTIVE
The organization of ribosomal RNA (rrn) operons in Lactobacillus sanfranciscensis was studied in order to establish an easy-to-perform method for identification of L. sanfranciscensis strains, based on the length and sequence polymorphism of the 16S-23S rDNA intergenic spacer region (ISR).


RESULTS
PCR amplification of the 16S-23S rDNA ISRs of L. sanfranciscensis gave three products distinguishing this micro-organism from the remaining Lactobacillus species. Sequence analysis revealed that two of the rrn operons were organized as in previously reported lactobacilli: large spacer (L-ISR), containing tRNA(Ile) and tRNA(Ala) genes; small spacer (S-ISR) without tRNA genes. The third described spacer (medium, M-ISR), original for L. sanfranciscensis, harboured a tRNA-like structure. An oligonucleotide sequence targeting the variable region between tDNA(Ile) and tDNA(Ala) of L. sanfranciscensis L-ISR was approved to be suitable in species-specific identification procedure. Analysis by pulse-field gel electrophoresis of the chromosomal digest with the enzyme I-CeuI showed the presence of seven rrn clusters. Lactobacillus sanfranciscensis genome size was estimated at c. 1.3 Mb.


CONCLUSIONS
Direct amplification of 16S-23S ISRs or PCR with specific primer derived from L-ISR showed to be useful for specific typing of L. sanfranciscensis. This was due to the specific rrn operon organization of L. sanfranciscensis strains.


CONCLUSIONS
In this paper, we have reported a rapid procedure for L. sanfranciscensis identification based on specific structures found in its rrn operon.
Valcheva
R
R
Laboratoire de Microbiologie Alimentaire et Industrielle, QM2A, ENITIAA, Nantes Cedex 3, France. development@tehra.com
Kabadjova
P
P
Rachman
C
C
Ivanova
I
I
Onno
B
B
Prévost
H
H
Dousset
X
X
D001483:Base Sequence / Q000235:genetics; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics*; D021901:DNA, Intergenic; D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D005516:Food Microbiology; D005798:Genes, Bacterial / Q000235:genetics; D007778:Lactobacillus / Q000235:genetics / Q000302:isolation & purification*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009876:Operon / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000379:methods*; D011110:Polymorphism, Genetic / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods; D013045:Species Specificity; D014158:Transcription, Genetic / Q000235:genetics
D017931:DNA Primers; D004269:DNA, Bacterial; D021901:DNA, Intergenic; D021903:DNA, Ribosomal Spacer; D012329:RNA, Bacterial; D012343:RNA, Transfer