Cognac distillation wines host specific Oenococcus oeni strains representing a novel genetic lineage

Oenococcus oeni is the lactic acid bacteria species best adapted to wine. It proliferates during alcoholic fermentation and typically becomes the most abundant species during malolactic fermentation. A large diversity of O. oeni strains is present in all wine-producing regions. These strains group into several genetic lineages, which are more product-specific rather than linked to geography. I. e. strains of one genetic lineage are often detected in the same wine type produced in distant regions. This study aimed to investigate the biodiversity of O. oeni involved in malolactic fermentations of Cognac wines produced for distillation. These wines have several specific characteristics: they are low-pH white wines, low in alcohol, produced without added sulfites, and from a single grape variety (Ugni blanc). Nearly 3500 O. oeni isolates were obtained from 132 wines collected from 24 cellars across the main cognac-producing areas. 458 different strains were identified by genotyping, representing in between 1 and 249 isolates. A distribution analysis showed a large diversity of strains in each wine and cellar. Forty-nine strains were sequenced and a phylogenomic tree was reconstructed including 247 previously published genomes of strains from other regions and products. This tree revealed a new genetic lineage harboring exclusively Cognac strains whose predominance on Cognac wines was further confirmed by a specifically developed quantitative PCR test. The results highlight the existence of a new sub-lineage indicative of the domestication of O. oeni strains to a single type of wine, and across an entire wine-producing region.