全基因组测序揭示两株泡菜源植物乳杆菌基因型差异和潜在益生特性

Whole-genome sequencing reveals genotypic differences and potential probiotic properties of two Paocai-derived Lactiplantibacillus plantarum strains

摘要:

【目的】为了探究植物乳杆菌(Lactiplantibacillus plantarum)基因型差异和潜在益生特性，采用全基因组测序技术对其进行测序并解析基因组序列及生物特性。【方法】本研究基于HiSeq和PacBio测序平台，对团队前期从四川多代泡菜中分离获得、体外益生特性评价良好的潜在益生菌菌株L. plantarum Eden-Star PC06和L. plantarum Eden-Star PC108的全基因组进行测序。利用相关生物信息学软件对原始数据进行组装及其后续的功能注释、分子进化、菌株安全性、次级代谢产物合成基因簇以及益生特性相关基因进行分析。【结果】通过基因组装得到了2株植物乳杆菌的全基因组信息，L. plantarum Eden-Star PC06和Eden-Star PC108基因组大小分别为3 163 902 bp和3 205 054 bp；GC含量分别为44.68%和44.67%；分别包含3 161个和3 197个DNA编码序列；功能基因数据库比对结果显示2株菌在碳水化合物利用、氨基酸利用和糖基转移酶等基因上得到大量注释；通过比对数据库，在2株植物乳杆菌全基因组上发现了4个与肠液耐受相关的胆盐水解酶基因、完整的植物乳杆菌细菌素合成相关基因簇和抵御多种胁迫的益生相关基因。【结论】本研究通过全基因组测序在基因水平上探究了L. plantarum Eden-Star PC06和Eden-Star PC108基因型差异和益生特性基因，证明L. plantarum Eden-Star PC06和Eden-Star PC108是2株有应用前景的益生菌菌株，以期为筛选优良益生菌菌株和评价其益生特性提供遗传学基础。

Abstract:

[Objective] To explore the genotypic differences and potential probiotic properties of Lactiplantibacillus plantarum by using whole genome sequencing technology. [Methods] Based on the HiSeq and PacBio, this study sequenced the potential probiotic strains L. plantarum Eden-Star PC06 and L. plantarum Eden-Star PC108 with good evaluation of in vitro probiotic properties isolated from Sichuan multi-generation Paocai in the previous study. The relevant bioinformatics software was used to assemble the raw data and analyze the subsequent functional annotation, molecular evolution, strain safety, secondary metabolite synthesis gene clusters, and probiotic-related genes. [Results] The whole-genome information of two L. plantarum strains was obtained through gene assembly, and the genome sizes of L. plantarum Eden-Star PC06 and Eden-Star PC108 were 3 163 902 bp and 3 205 054 bp, respectively. The GC content of Eden-Star PC06 and Eden-Star PC108 was 44.68% and 44.67%, respectively, and they contained 3 161 and 3 197 DNA coding sequences, respectively. The comparison results of functional gene database showed that the two strains were extensively annotated on genes such as carbohydrate utilization, amino acid utilization, and glycosyltransferase. We found four genes related to intestinal fluid tolerance, intact gene clusters related to bacteriocin synthesis of L. plantarum, and probiotic genes resistant to multiple stresses on the whole genome of two strains of L. plantarum in the comparison database. [Conclusion] This study explores the genotypic differences and potential probiotic properties of two L. plantarum strains Eden-Star PC06 and Eden-Star PC108 at the gene level by whole-genome sequencing, and it has proved that L. plantarum Eden-Star PC06 and Eden-Star PC108 are potential probiotic strains with promising applications. This study is expected to provide a genetic basis for screening out excellent probiotic strains and evaluating their probiotic properties.