弯曲乳杆菌与清酒乳杆菌的比较基因组学分析

Comparative Genomic Analysis of Latilactobacillus curvatus and L.sakei

本研究对19株弯曲乳杆菌(Latilactobacillus curvatus)和40株清酒乳杆菌(L.sakei)的基因组进行了比较分析。平均核苷酸同一性及全基因组共线性分析表明,L.curvatus和L.sakei基因组间的核酸序列同源性较弱,可作为区分两个物种的指标。对两个物种分别构建泛基因组,并对泛基因组中的核心基因功能进行注释。结果显示,L.curvatus和L.sakei各自的核心基因组主要涉及菌株的基础代谢。对菌株个体基因组的比对分析发现:1)L.curvatus与L.sakei均含有广泛的糖苷水解酶类编码基因,在分解和代谢膳食纤维类多糖、乳糖利用以及木质纤维素中具有丰富的基因资源;2)3个菌株含抗生素耐药性基因,且来源于基因横向转移;3)L.sakei特有的精氨酸脱亚胺酶途径、L.curvatus中的丝氨酸脱水酶途径及鸟嘌呤脱氨酶途径,以及个别菌株中谷氨酸脱羧酶的发掘,揭示了这两类菌不同的抗酸机制;4)冷应激蛋白编码基因的发现也赋予了这两类菌良好的冷加工特性。此外,部分L.sakei基因组中含有编码lactocin S及凝结素相关的基因簇。总之,本研究通过对L.curvatus及L.sakei进行基因组水平的比较和分析,提供了两个物种之间的分类标准以及菌株个体上的差异信息,为这两种乳酸菌的生理生化分子遗传机制研究以及工业应用奠定了基础。

In this study,the genomes of 19 Latilactobacillus curvatus and 40 L.sakei strains were comparatively analyzed.Average nucleic acid identity(ANI)and genome-wide colinearity indicated that the genomes of L.curvatus and L.sakei had weak nucleotide sequence homology,allowing them to be used as indicators to distinguish the two species.Pangenomes for these species were constructed,whose core gene functions were annotated.The results showed that the core genomes of L.curvatus and L.sakei were mainly involved in their basic metabolism.Analysis of individual genomes of the strains revealed that 1)both L.curvatus and L.sakei contained a wide range of genes encoding glycoside hydrolases,which are abundant genetic resources for catabolizing and metabolizing dietary fiber such as polysaccharides,lactose utilization,and lignocellulose;2)antibiotic resistance genes were annotated in the genomes of three strains,which originate from horizontal gene transfer;3)the unique arginine deiminase pathway of L.sakei,the serine dehydratase and guanine deaminase pathways of L.curvatus,and the glutamate decarboxylase pathway of several strains were identified,revealing that the acid tolerance mechanisms of these two species are different;and 4)genes encoding cold stress proteins were discovered,which endow the two species with good cold processing properties.Moreover,the genomes of some L.sakei strains contained gene clusters related to the biosynthesis of lactocin S and condensin.In conclusion,this study established taxonomic criteria for the two species and information on individual differences between their strains,which will provide a basis for the study of the physiological,biochemical,molecular genetic mechanisms of L.curvatus and L.sakei and their industrial applications.