副格氏乳杆菌IMAU FB017的遗传背景和益生相关基因分析

Genetic background and analysis of probiotics related genes in Lactobacillus paragasseri IMAU FB017

摘要:

【目的】副格氏乳杆菌(Lactobacillus paragasseri)作为格式乳杆菌(Lactobacillus gasseri)的近源物种，是肠道、生殖道重要菌种之一。本研究团队前期发现L. paragasseri IMAU FB017具有良好的胃酸和胆盐耐受性，拟从基因组水平解析IMAU FB017的遗传背景和功能基因特征，并挖掘潜在益生特性基因，为其开发利用奠定遗传学基础。【方法】采用Nanopore和Illumina两种测序技术完成了IMAU FB017全基因组测序及完成图组装，并结合NCBI已公开的18株L. paragasseri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IMAU FB017基因组特征。【结果】结果显示IMAU FB017基因组包含1条环状染色体和1个质粒，其中环状染色体大小为1 880 023 bp，GC含量为34.90%，包含1 851个蛋白质编码区(protein-coding sequence, CDS)；质粒大小43 639 bp，GC含量为38.00%。基于18株L. paragasseri基因组序列识别到的903个核心基因构建系统发育树，发现L. paragasseri群体共形成3个分支。菌株IMAU FB017属于分支Ⅰ，该分支包含菌株最多(13株，约占68%)，且相同分离源的菌株无显著聚集趋势。功能注释分析发现，IMAU FB017基因组中编码关于N-乙酰半乳糖胺和半乳糖胺的利用相关基因以及草酸分解代谢相关益生基因，并且包含1条完整的胞外多糖(exopolysaccharides,eps)基因簇和3条耐酸耐胆盐相关基因簇且与表型对应。【结论】本研究从基因组水平解析了IMAU FB017遗传背景，并挖掘了潜在益生相关基因，为其开发利用提供参考。

Abstract:

[Objective] Lactobacillus paragasseri as a closely related species of L. gasseri, is one of the important bacteria in the intestinal and reproductive tract. Our research team previously found that L. paragasseri IMAU FB017 had good tolerance to stomach acid and bile salt. Therefore, we intended to analyze the genetic background of IMAU FB017 from the genome level, explore its functional gene characteristics, and dig into its potential probiotic genes, thereby laying a genetic foundation for its development and utilization. [Methods] In this study, the whole genome of IMAU FB017 was sequenced and assembled using Nanopore and Illumina sequencing technologies, and the genomic sequences of 18 L. paragasseri strains published by National Center for Biotechnology Information (NCBI) were combined for comparative genomic analysis. Roary software was used to identify core gene sets and pan gene sets. The Rapid Annotation using Subsystem Technology website was used for functional annotation of the genome to explore the genomic characteristics of IMAU FB017. [Results] The results showed that IMAU FB017 genome contained a ring chromosome and a plasmid, and the size of the ring chromosome was 1 880 023 bp, with 34.90% of the guanine/cytosine (G/C) content, containing 1 851 protein-coding sequences. The size of the plasmid was 43 639 bp, and the G/C content was 38.00%. A phylogenetic tree was constructed based on 903 core genes identified from 18 L. paragasseri genome sequences. It was found that L. paragasseri population formed three clades. Strain IMAU FB017 belonged to clades Ⅰ, which contained the most strains (13 strains, about 68%), and the strains from the same source had no significant aggregation trend. Functional annotation analysis found that the IMAU FB017 genome encoded genes related to N-acetylgalactosaamine and galactosaamine utilization, as well as probiotic genes related to oxalate catabolism, and contained a complete exopolysaccharide (EPS) gene cluster and three acid and bile salt tolerance gene clusters corresponding to the phenotype. [Conclusion] In this paper, the genetic background of IMAU FB017 has been analyzed at the genomic level, and the potential probiotic genes have been mined to provide references for its development and utilization.