A NEW SPECIFIC LINEAGE OF OENOCOCCUS OENI IN COGNAC APPELLATION WINES

Abstract

Oenococcus oeni is the main lactic acid bacteria (LAB) species which conducts the malolactic fermentation (MLF) in wine. During MLF, O. oeni converts malic acid into lactic acid, which modulates wine aroma composition leading to better balanced organoleptic properties. O. oeni is a highly specialized species only detected in environments containing alcohol such as wine, cider or kombucha. Genome analysis of more than 240 strains showed that they form at least 4 main phylogenetic lineages and several sublineages, which are associated with different beverages or types of wines. Distilled wines produced in Cognac appellation of origin undergo MLF. Given the lack of knowledge of LAB present in distillation wines, the control of MLF and the further storage of wines is a difficult task. Therefore, the aim of this work is to analyze the biodiversity of O. oeni strains naturally occurring in cognac distilled wines and to determine if they confer a particular quality to the spirit after distillation.
559 samples of wines were collected before, during and after MLF from 24 wineries located in almost all the regions of Cognac appellation during 4 vintages from 2019 to 2022. The samples were processed to isolate single colonies of LAB, which were typed at the species and strain levels by MLVA (Multiple Loci of Variable Number of Tandem Repeats Analysis). About 5000 colonies of O. oeni isolates were obtained and assigned to 688 different strains. The most abundant strains in each winery were further analyzed at the genomic level. A total of 49 draft genomes were produced by Illumina MiSeq. The distances between these 49 genomes and 240 other publicly available O. oeni genomes were calculated using ANI (Average Nucleotide Identity) and used to reconstruct a phylogenetic tree. The tree showed that 34 of the 49 strains grouped together in a new phylogenetic lineage and contain only stains isolated from cognac wines. The 34 strains of this lineage represented more than half of the colonies isolated during MLF in the wineries, which suggests that this lineage is specific and predominant in all the cognac wines. Moreover, the same strains were often found in the same wineries during consecutive vintages. The results suggest that the strains of this genetic lineage share specific genetic properties conferring them a better adaptation to cognac wines, and may in addition confer specific aromatic characteristics to cognac wines during MLF.