Phenolic compounds are important components of wine and are known to have an impact on the physiology of wine microbes. The influence of specific sub-sets of phenolic compounds on the growth and metabolism of lactic acid bacteria (LAB) and on the diversity of Oenococcus oeni in inoculated and non-inoculated red wines was investigated during malolactic fermentation (MLF) and subsequent storage. Representative O. oeni strains from wines treated with flavonols and trans-resveratrol were isolated and analyzed by pulsed-field gel electrophoresis of rare restriction enzyme digests (REA-PFGE). 28 days after MLF initiation, strains from all samples had entered the death phase, except those supplemented with trans-resveratrol. In the non-inoculated samples, the onset of lactic acid production was apparently delayed by all compounds tested, except for the flavan-3-ols. Increased levels of phenolics also delayed citrate consumption in inoculated samples. PFGE analysis revealed 22 genetic profiles, and some profiles were characteristics of specific samples. The commercial starter used in the inoculated wines did not dominate during MLF. The effect of the phenolics studied was dependent on the origin and concentration of each as well, as the fermentation stage and whether the wines were inoculated. The effect of flavonols and trans-resveratrol seemed to be strain-dependent, which could have implications on the final quality of wines.Fermentation 2019, 5, 1 2 of 17 chosen according to their technological or quality attributes. As a consequence of their adaptation to the wine environment, in particular, their tolerance to wine's acidity and alcohol concentration, strains of O. oeni are the predominant LAB responsible for the MLF. Thus, starter cultures for the MLF are also predominantly selected from this species. The strain-level diversity of O. oeni populations in wine ecosystems is very high, and it can be region-and winery-specific [6,7], often contributing to recognized differences in wines. O. oeni has been shown to genetically adapt according the type of wine (white or red), driven by the pH and the phenolic compounds present [8].Taxonomically, the species is ordered into three groups, with A and B being the two major phylogenetic groups, and C a putative group composed of a unique strain isolated from cider. Group A exclusively contains strains found in wine. All strains from cider, except that attributed to group C, are located in group B, while strains from Champagne and Burgundy are only from group A. It appears that most of the strains isolated from malolactic ferments derive from the domestication of ancestral O. oeni strains during the process of the industrialization of wine and cider, rather than responding to geographical constraints [9][10][11].Several molecular techniques have been applied to determine the diversity of LAB in red wines. Polymerase chain reaction (PCR) -based techniques including 16S metabarcoding sequencing [12], PCR-DGGE (denaturing gradient gel electrophoresis) [13] and species-specific mul...