Oenococcus oeni is an environmental lactic acid bacteria species encountered particularly in wine, where it achieves the malolactic fermentation. Molecular typing methods have previously revealed that the species is made of several genetic groups of strains, some being specific to certain types of wines, ciders or regions. Here, we describe 36 recently released O. oeni genomes and the phylogenomic analysis of these 36 plus 14 previously reported genomes. We also report three genome sequences of the sister species Oenococcus kitaharae that were used for phylogenomic reconstructions. Phylogenomic and population structure analyses performed by diverse methods revealed that the 50 O. oeni genomes delineate two major groups of 12 and 37 strains, respectively named A and B, plus a putative group C consisting in a single strain. Strains of genetic groups A/B and C were more distantly related than strains from different subspecies of Leuconostoc mesenteroides. In addition, group A strains proved to be predominant in wine and to form subgroups adapted to specific types of wine such as champagne. The orthologs and SNP contents of the diverse genetic groups revealed some of their specific genetic features. Altogether, the results confirmed that the O. oeni species is made of several genetic groups of strains, whose adaptation to different products such as champagne or cider is reflected at the genetic level. They also suggest that ancestral strains were adapted to low-ethanol containing environments such as fruits and that group A strains were naturally selected in a process of domestication to wine.

Phylogenomic analysis of Oenococcus oeni reveals specific domestication of strains to cider and wines

SPANO, GIUSEPPE;
2015-01-01

Abstract

Oenococcus oeni is an environmental lactic acid bacteria species encountered particularly in wine, where it achieves the malolactic fermentation. Molecular typing methods have previously revealed that the species is made of several genetic groups of strains, some being specific to certain types of wines, ciders or regions. Here, we describe 36 recently released O. oeni genomes and the phylogenomic analysis of these 36 plus 14 previously reported genomes. We also report three genome sequences of the sister species Oenococcus kitaharae that were used for phylogenomic reconstructions. Phylogenomic and population structure analyses performed by diverse methods revealed that the 50 O. oeni genomes delineate two major groups of 12 and 37 strains, respectively named A and B, plus a putative group C consisting in a single strain. Strains of genetic groups A/B and C were more distantly related than strains from different subspecies of Leuconostoc mesenteroides. In addition, group A strains proved to be predominant in wine and to form subgroups adapted to specific types of wine such as champagne. The orthologs and SNP contents of the diverse genetic groups revealed some of their specific genetic features. Altogether, the results confirmed that the O. oeni species is made of several genetic groups of strains, whose adaptation to different products such as champagne or cider is reflected at the genetic level. They also suggest that ancestral strains were adapted to low-ethanol containing environments such as fruits and that group A strains were naturally selected in a process of domestication to wine.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11369/327527
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