Evaluation of three PCR primers based on the 16S rRNA gene for the identification of lactic acid bacteria from dairy origin

Abstract

Partial sequencing of 16S ribosomal RNA (rRNA) gene is commonly used for the identification of lactic acid bacteria (LAB). The present study evaluated the performance in the identification of dairy LAB of two universal (515FPL-13B and 91E-13) and one Lactobacillus group-specific (S-D-Bact-0011-a-S-17-S-G-Lab-0677-a-A-17) primer pairs. After amplification, the 16S rRNA gene portions were sequenced, and sequences were analysed using the Ribosomal Database Project (RDP-II) and Basic Length Alignment Search Tool (BLAST) programs. The primers were used with three reference strains and eight isolates from Oaxaca cheese. The 515FLP-13B primer misled the identification of one reference strain and two isolates. Five among the eight isolates were identified as Lactococcus lactis by at least two of the primers, and the specific primer showed higher RDP-II identity scores than the universal primers. The specific primer was successfully used for the identification of other 24 cheese isolates. The joint use of the two programs (RDP-II and BLAST) allowed to confirm the identification results.