Multiplex variable number of tandem repeats for Oenococcus oeni and applications

•A multiplex fragment length analysis (FLA) method was developed based on five polymorphic loci of the Oenococcus oeni genome.•FLA proved to be robust, accurate, fast, and easy to perform.•FLA was associated with phenotypic and genotypic characters to construct predictive models.

Oenococcus oeni is responsible for the malolactic fermentation of wine. Genomic diversity has already been established in this species. In addition, winemakers usually report varying starter-culture efficiency. It is essential to monitor indigenous and selected strains in order to understand strain survival and development during the winemaking process. A previous article described a variable number of tandem repeats (VNTR) scheme, based on five polymorphic loci of the genome. VNTR typing of O. oeni was highly discriminating, faster, and more reliable than the PFGE or MLST methods. The objective of this study was to set up a faster protocol by multiplexing, taking advantage of the high performance of multicolor capillary electrophoresis. The primers were labeled with multiple fluorescent dyes. PCR conditions were adapted by multiplexing amplifications in two separate PCR mixtures for the five loci, both at the same annealing temperature. The resulting assay proved to be robust, accurate, fast and easy to perform. Thanks to this new protocol, all O. oeni strains used in the study were typed using the five tandem repeats (TR). As expected, the primers for the five TR loci were specific to O. oeni. The method was improved to analyze isolated and mixed colonies, as well as bacteria harvested from wine using fast technology for analysis of nucleic acids (FTA®) technology. Finally, predictive models were constructed, to predict phylogenetic relationships and associate bacterial strain resistance to freeze-drying with fragment length analysis (FLA) profiles and genotypic and phenotypic characters.