Limosilactobacillus fermentum F-6的遗传背景和功能基因组

Genetic background and functional genome of Limosilactobacillus fermentum F-6

摘要:

【目的】Limosilactobacillus fermentum具有增强免疫力、产胞外多糖(exopolysaccharide,EPS)等多种功能特性,广泛应用于食品领域,具有较高经济价值。本文从群体遗传学角度,解析L. fermentum F-6的遗传背景和功能基因特征,为其开发利用提供遗传学基础。【方法】本研究对NCBI已公开的23株L. fermentum全基因组序列和1株模式菌株ATCC 14931^T的基因组序列进行比较基因组学分析。利用Roary软件识别核心基因集与泛基因集;采用rapid annotation using subsystem technology (RAST)网站对基因组进行功能注释,以探究F-6基因组特征。【结果】以识别到的997个核心基因构建系统发育树,发现聚类趋势与分离源无关,但F-6与3株食品分离株聚在同一分支。功能注释分析发现,24株L. fermentum中仅F-6含有参与支链氨基酸合成途径的基因(ilvD、leuA等),可为机体提供必需氨基酸。F-6含有大量编码糖基转移酶和UDP-葡萄糖4-表异构酶的基因,且含有1个完整的eps基因簇。与其他L. fermentum相比,F-6携带的特有功能基因gadC与菌株耐酸能力有关。此外,F-6具有与谷胱甘肽、抗菌肽和黏附分子合成相关的功能基因。【结论】本文从全基因组水平解析L. fermentum F-6遗传背景和功能基因特征,认为其是一株具有耐酸基因、支链氨基酸合成基因和完整eps基因簇的潜在益生菌株,为其应用研究提供了必要的理论依据。

关键词:Limosilactobacillus fermentum F-6;比较基因组学;遗传背景;功能基因;eps基因簇

Abstract:

[Objective] Enhancing immunity and producing exopolysaccharide (EPS),Limosilactobacillus fermentum is widely used in food industry and is of huge economic value.Based on population genetics,this paper aims to analyze the genetic background and functional gene characteristics of L. fermentum F-6,which is expected to lay a genetic basis for the development and utilization of the strain.[Methods] Comparative genomics was used to analyze the whole-genome sequences of 23 L. fermentum strains and 1 model strain ATCC 14931^T from NCBI,Roary to identify core-pan genes,and rapid annotation using subsystem technology (RAST) to annotate the genomes.[Results] A phylogenetic tree was constructed based on the yielded 997 core genes and the analysis showed that the clustering had nothing to do with the source.However,strain F-6 was in the same clade with 3 food-derived strains.Genome annotation results revealed that only strain F-6 contained genes involved in branched chain amino acid synthesis pathway (ilvD,leuA,etc.) and thus can provide essential amino acids for the body.Strain F-6 harbored a large number of genes encoding glycosyltransferases and UDP-glucose 4-epimerase,and contained a complete eps cluster.Compared with other L. fermentum strains,strain F-6 had the unique functional gene gadC which is associated to acid resistance.In addition,potential probiotic genes such as genes related to the synthesis of glutathione,antimicrobial peptide,and adhesion molecules were also identified in the genome.[Conclusion] According to the genomic background and functional genome,F-6 is a potential probiotic strain with acid resistance genes,branched chain amino acid synthesis genes,and a complete eps gene cluster,which will contribute to our understanding of the genetic basis of L. fermentum F-6.

Key words:Limosilactobacillus fermentum F-6;comparative genomics;genetic background;functional genes;eps cluster