Comparison of phenotypic (Biolog System) and genotypic (random amplified polymorphic DNA-polymerase chain reaction, RAPD-PCR, and amplified fragment length polymorphism, AFLP) methods for typing Lactobacillus plantarum isolates from raw vegetables and fruits

The diversity of 72 isolates of Lactobacillusplantarum, previously identified from different rawvegetables and fruits, was studied based on phenotypic (BiologSystem) and genotypic (randomly amplifiedpolymorphicDNA-polymerasechainreaction, RAPD-PCR, and amplifiedfragmentlengthpolymorphism, AFLP) approaches. A marked phenotypic and genotypic variability was found. Eight clusters were formed at the similarity level of 92% based on BiologSystem analysis. The most numerous clusters grouped isolates apart from the original habitat. Almost all isolates fermented maltose, d,l-lactic acid, N-acetyl-d-mannosamine and dextrin, and other typical carbon sources which are prevalent in rawvegetables and fruits. None of the isolates fermented lactose and free amino acids. At high values of linkage distance, two main clusters were obtained from both UPGMA (unweighted pair group with arithmetic average) dendrograms of RAPD-PCR and AFLP analyses. The two clusters mainly separated isolates from tomatoes and carrots from those isolated from pineapples. At 2.5 linkage distance, a high polymorphism was found and several sub-clusters were formed with both analyses. In particular, AFLP allowed the differentiation of 55 of the 72 isolates of L. plantarum. The discriminatory power of each technique used was calculated through the Simpson's index of diversity (D). The values of the D index were 0.65, 0.92 and 0.99 for BiologSystem, RAPD-PCR and AFLP analyses, respectively