CERELA-CONICET, Centro de Referencia para Lactobacilos, San Miguel de Tucumán, Argentina.
MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, Jouy-en-Josas, France.
Genome Biol Evol. 2018 Jun 1;10(6):1516-1525. doi: 10.1093/gbe/evy106.
Lactobacillus curvatus is a lactic acid bacterium encountered in many different types of fermented food (meat, seafood, vegetables, and cereals). Although this species plays an important role in the preservation of these foods, few attempts have been made to assess its genomic diversity. This study uses comparative analyses of 13 published genomes (complete or draft) to better understand the evolutionary processes acting on the genome of this species. Phylogenomic analysis, based on a coalescent model of evolution, revealed that the 6,742 sites of single nucleotide polymorphism within the L. curvatus core genome delineate two major groups, with lineage 1 represented by the newly sequenced strain FLEC03, and lineage 2 represented by the type-strain DSM20019. The two lineages could also be distinguished by the content of their accessory genome, which sheds light on a long-term evolutionary process of lineage-dependent genetic acquisition and the possibility of population structure. Interestingly, one clade from lineage 2 shared more accessory genes with strains of lineage 1 than with other strains of lineage 2, indicating recent convergence in carbohydrate catabolism. Both lineages had a wide repertoire of accessory genes involved in the fermentation of plant-derived carbohydrates that are released from polymers of α/β-glucans, α/β-fructans, and N-acetylglucosan. Other gene clusters were distributed among strains according to the type of food from which the strains were isolated. These results give new insight into the ecological niches in which L. curvatus may naturally thrive (such as silage or compost heaps) in addition to fermented food.
短乳杆菌是一种在许多不同类型的发酵食品（肉类、海鲜、蔬菜和谷物）中发现的乳酸杆菌。尽管该物种在这些食品的保存中起着重要作用，但很少有人试图评估其基因组多样性。本研究使用 13 个已发表基因组（完整或草图）的比较分析，以更好地了解作用于该物种基因组的进化过程。基于进化的合并模型的系统发育分析表明，L. curvatus 核心基因组中 6742 个单核苷酸多态性位点将两个主要群体分开，第 1 谱系由新测序的菌株 FLEC03 代表，第 2 谱系由模式菌株 DSM20019 代表。这两个谱系还可以通过它们的辅助基因组内容来区分，这揭示了一个长期的依赖谱系的遗传获得的进化过程，以及种群结构的可能性。有趣的是，来自第 2 谱系的一个分支与第 1 谱系的菌株共享更多的辅助基因，而不是与第 2 谱系的其他菌株共享，这表明碳水化合物代谢的近期趋同。两个谱系都有广泛的与植物来源的碳水化合物发酵有关的辅助基因，这些基因是从 α/β-葡聚糖、α/β-果聚糖和 N-乙酰葡糖胺的聚合物中释放出来的。其他基因簇根据菌株分离自哪种食物而分布在菌株中。这些结果为 L. curvatus 可能自然存在的生态位（如青贮或堆肥堆）提供了新的见解，除了发酵食品之外。
