Lactobacillus reuteri YSJL-12 was isolated from healthy sow fresh feces and used as probiotics additives previously. To investigate the genetic basis on probiotic potential and identify the genes in the strain, the complete genome of YSJL-12 was sequenced. Then comparative genome analysis on 9 strains of Lactobacillus reuteri was performed. The genome of YSJL-12 consisted of a circular 2,084,748 bp chromosome and 2 circular plasmids (51,906 and 15,134 bp). From among the 2065 protein-coding sequences (CDSs), the genes resistant to the environmental stress were identified. The function of COG (Clusters of Orthologous Group) protein genes was predicted, and the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were analyzed. The comparative genome analysis indicated that the pan-genome contained a core genome of 1257 orthologous gene clusters, an accessory genome of 1064 orthologous gene clusters, and 1148 strain-specific genes, and the antibacterial mechanism among Lactobacillus reuteri strains might be different. The phylogenetic analysis and genomic collinearity revealed that the phylogenetic relationship among 9 strains of Lactobacillus reuteri was connected with host species and showed host specificity. The research could help us to better predict genes function and understand genetic basis on adapting to host gut in Lactobacillus reuteri YSJL-12.

从健康母猪新鲜粪便中分离出路氏乳杆菌YSJL-12，以前用作益生菌添加剂。为了研究益生菌潜力的遗传基础并鉴定菌株中的基因，对YSJL-12的完整基因组进行了测序。然后比较9株罗伊氏乳杆菌的基因组分析被执行了。YSJL-12的基因组由一个2,084,748 bp环状染色体和2个环状质粒（51,906和15,134 bp）组成。从2065个蛋白质编码序列（CDS）中，鉴定了对环境胁迫具有抗性的基因。预测了COG（直系同源群）蛋白基因的功能，并分析了KEGG（基因和基因组京都百科全书）途径。比较基因组分析表明，该泛基因组包含一个核心基因组，其核心基因组为1257个直系同源基因簇，一个辅助基因组为1064个直系同源基因簇，以及1148个菌株特异性基因，以及罗伊氏乳杆菌的抗菌机制。菌株可能有所不同。系统发育分析和基因共线性表明，9株罗伊氏乳杆菌菌株之间的系统发生关系与宿主物种有关，并显示出宿主特异性。这项研究可以帮助我们更好地预测基因功能，并了解适应罗伊氏乳杆菌YSJL-12宿主肠道的遗传基础。