Campbell-Sills Hugo, El Khoury Mariette, Favier Marion, Romano Andrea, Biasioli Franco, Spano Giuseppe, Sherman David J, Bouchez Olivier, Coton Emmanuel, Coton Monika, Okada Sanae, Tanaka Naoto, Dols-Lafargue Marguerite, Lucas Patrick M
Univ. Bordeaux, ISVV, EA 4577 Œnologie, Villenave d'Ornon, France Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.
Univ. Bordeaux, ISVV, EA 4577 Œnologie, Villenave d'Ornon, France.
Genome Biol Evol. 2015 May 14;7(6):1506-18. doi: 10.1093/gbe/evv084.
Oenococcus oeni is a 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 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 of a single strain. A study on the orthologs and single nucleotide polymorphism contents of the genetic groups revealed that the domestication of some strains to products such as cider, wine, or champagne, is reflected at the genetic level. While group A strains proved to be predominant in wine and to form subgroups adapted to specific types of wine such as champagne, group B strains were found in wine and cider. The strain from putative group C was isolated from cider and genetically closer to group B strains. The results suggest that ancestral O. oeni strains were adapted to low-ethanol containing environments such as overripe fruits, and that they were domesticated to cider and wine, with group A strains being naturally selected in a process of further domestication to specific wines such as champagne.
酒酒球菌是一种特别常见于葡萄酒中的乳酸菌，它能进行苹果酸-乳酸发酵。分子分型方法此前已揭示，该物种由几个遗传菌株组构成，其中一些特定于某些类型的葡萄酒、苹果酒或地区。在此，我们描述了最近公布的36个酒酒球菌基因组，以及对这36个基因组与之前报道的14个基因组的系统基因组分析。我们还报告了用于系统基因组重建的姊妹物种北原酒球菌的三个基因组序列。进行的系统基因组和群体结构分析显示，50个酒酒球菌基因组分别勾勒出两个主要组，一组有12个菌株，另一组有37个菌株，分别命名为A组和B组，外加一个假定的C组，由单个菌株组成。一项关于这些遗传组直系同源基因和单核苷酸多态性含量的研究表明，一些菌株对苹果酒、葡萄酒或香槟等产品的驯化在基因层面有所体现。虽然A组菌株在葡萄酒中占主导地位，并形成了适应特定类型葡萄酒（如香槟）的亚组，但B组菌株在葡萄酒和苹果酒中均有发现。假定C组的菌株是从苹果酒中分离出来的，在基因上更接近B组菌株。结果表明，酒酒球菌的祖先菌株适应于低乙醇含量的环境，如过熟水果，并且它们被驯化为用于苹果酒和葡萄酒，其中A组菌株在进一步驯化为特定葡萄酒（如香槟）的过程中被自然选择。
