副地衣芽孢杆菌FA6全基因组测序及比较基因组学分析

WHOLE GENOME SEQUENCING AND COMPARATIVE ANALYSIS OF BACILLUS PARALICHENIFORMIS FA6 STRAIN

  • 摘要: 副地衣芽孢杆菌(Bacillus paralicheniformis)FA6是一株从草鱼肠道内分离出来的细菌, 其具有淀粉酶和纤维素酶等多种碳水化合物酶活性。为深入研究副地衣芽孢杆菌FA6可能的益生机制, 研究通过三代测序技术测定了副地衣芽孢杆菌FA6的全基因组序列, 运用生物信息学方法进行基因组组装、基因预测和功能注释。同时通过比较基因组学方法, 比较分析了副地衣芽孢杆菌FA6与4株基因组序列已经发表的芽孢杆菌基因组结构和功能的差异。结果发现副地衣芽孢杆菌FA6全基因组由1条环状染色体组成, 大小为4450579 bp, GC含量为45.9%。副地衣芽孢杆菌FA6基因组中含有128个蛋白酶基因, 32个脂肪酶基因和72个糖苷水解酶基因, 这些基因与食物降解相关; 此外, 细菌基因组中还含有7个编码羊毛硫抗生素相关的基因。比较基因组结果显示, 副地衣芽孢杆菌FA6与其他4株芽孢杆菌的基因组共线性关系较好, 但是与地衣芽孢杆菌菌株相比, 菌株FA6基因组特征更接近于副地衣芽孢杆菌菌株。副地衣芽孢杆菌FA6基因组中编码纤维素酶、半纤维素酶和淀粉酶的基因数量分别为5、7和5个, 多于其他菌株, 能够更好地降解植物多糖。研究结果表明副地衣芽孢杆菌FA6高度适应植物性成分, 反映了该菌株在草鱼肠道中的适应性进化, 该菌株可能可以作为益生菌用于水产养殖。

     

    Abstract: Previous studies have shown that Bacillus paralicheniformis FA6 strain (FA6), isolated from the intestine of grass carp, has a role in the degradation of various carbohydrates (e.g. amylase or cellulase activity). In order to study the putative mechanisms of action and explore its potential as a probiotic, we used the third-generation sequencing technology to determine its whole genome sequence. Genome assembly, gene prediction and functional annotation were performed by using bioinformatics methods. Besides, we conducted structural and functional comparative genomic analyses between B. paralicheniformis FA6 and four other available Bacillus spp. genomes (two B. paralicheniformis and two B. licheniformis). Sequence analysis showed that the genome of B. paralicheniformis FA6 consists of a single chromosome, with the size of 4450579 bp, and the GC content of 45.9%. The B. paralicheniformis FA6 genome contains multiple food digestion-related genes, including 128 protease genes, 32 lipase genes and 72 glycoside hydrolase genes. In addition, the bacterial genome contains seven genes encoding for lantibiotics. Structural comparative analysis revealed that all five Bacillus spp. genomes share a collinear structural relationship, but genomic features of B. paralicheniformis FA6 are most similar to the two conspecifics. A comparison of metabolic pathways (KEGG) among the five Bacillus spp. strains showed that B. paralicheniformis FA6 has the largest number of genes involved in metabolic and environmental information processing. The numbers of genes in the B. paralicheniformis FA6 genome encoding cellulases, hemicellulases and amylases were 5, 7 and 5 respectively. This is higher than in other four strains, which indicates that B. paralicheniformis FA6 is better adapted for the digestion of plant cell wall polysaccharides. The results of this study indicate that B. paralicheniformis FA6 is highly adapted for the utilization of a broad range of plant metabolites, which may be a reflection of its adaptive evolution in the intestinal tract of grass carp. Moreover, the results of this study will provide a theoretical basis for the application of B. paralicheniformis FA6 as a dietary supplement to aquaculture feed.

     

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