Xu Su, Cheng Jianjun, Meng Xiangchen, Xu Yan, Mu Ying
College of Food Science, Northeast Agricultural University, Harbin, China.
Evol Bioinform Online. 2020 Jul 27;16:1176934320942192. doi: 10.1177/1176934320942192. eCollection 2020.
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 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 strains might be different. The phylogenetic analysis and genomic collinearity revealed that the phylogenetic relationship among 9 strains of 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 YSJL-12.
YSJL-12先前从健康母猪的新鲜粪便中分离出来，并用作益生菌添加剂。为了研究其益生菌潜力的遗传基础并鉴定该菌株中的基因，对YSJL-12的全基因组进行了测序。然后对9株该菌进行了比较基因组分析。YSJL-12的基因组由一个2,084,748 bp的环状染色体和两个环状质粒（51,906和15,134 bp）组成。从2065个蛋白质编码序列（CDS）中，鉴定出对环境胁迫有抗性的基因。预测了直系同源群（COG）蛋白质基因的功能，并分析了京都基因与基因组百科全书（KEGG）通路。比较基因组分析表明，泛基因组包含1257个直系同源基因簇的核心基因组、1064个直系同源基因簇的辅助基因组和1148个菌株特异性基因，并且这些菌株之间的抗菌机制可能不同。系统发育分析和基因组共线性显示，9株该菌之间的系统发育关系与宿主物种相关，并表现出宿主特异性。该研究有助于我们更好地预测基因功能，并了解YSJL-12适应宿主肠道的遗传基础。
