Abstract
Background Oenococcus oeni is the bacterial species that drives malolactic fermentation in most wines. Several studies have described a high intraspecific diversity regarding carbohydrate degradation abilities but the link between the phenotypes and the genes and metabolic pathways has been poorly described.ResultsA collection of 41 strains whose genomic sequences were available and representative of the species genomic diversity was analyzed for growth on 18 carbohydrates relevant in wine. The most frequently used substrates (more than 75% of the strains) were glucose, trehalose, ribose, cellobiose, mannose and melibiose. Fructose and L-arabinose were used by about half the strains studied, sucrose, maltose, xylose, galactose and raffinose were used by less than 25% of the strains and lactose, L-sorbose, L-rhamnose, sorbitol and mannitol were not used by any of the studied strains. To identify genes and pathways associated with carbohydrate catabolic abilities, gene-trait matching and a careful analysis of gene mutations and putative complementation phenomena were performed.ConclusionsFor most consumed sugars, we were able to propose putatively associated metabolic pathways. Most associated genes belong to the core genome. O. oeni appears as a highly specialized species, ideally suited to fermented fruit juice and more specifically to wine for a subgroup of strains.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3338-2) contains supplementary material, which is available to authorized users.
Highlights
Oenococcus oeni is the bacterial species that drives malolactic fermentation in most wines
Most associated genes belong to the core genome
We assessed the diversity of a representative subset of 41 O. oeni strains, regarding the ability to grow by using specific carbohydrates, and we identified the genomic elements that may direct the metabolic activities involved in the phenotypic differences in the 41 studied strains
Summary
Oenococcus oeni is the bacterial species that drives malolactic fermentation in most wines. Oenococcus oeni is considered the bacterial species most fitted to the particular conditions of winemaking [1, 2]. Wine undergoing the malolactic fermentation (MLF) is its main known ecological niche [3, 4], followed by cider and other fermented fruit [3]. In wine, it ferments the residual carbohydrates left by the yeasts at the end of the alcoholic fermentation and transforms malic acid into lactic acid [3].
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