该研究团队前期从健康婴儿粪便分离得到有较好耐酸耐胆盐能力的两歧双歧杆菌(Bifidobacterium bifidum)B1628,其灭活菌体可以缓解炎症性肠病(inflammatory bowel disease, IBD)小鼠结肠炎症性水肿,具有潜在应用价值。该研究基于生物信息学分析探究B.bifidum B1628的遗传背景和潜在益生基因,为其开发应用提供理论指导。对B.bifidum B1628进行Illumina与Oxford Nanopore结合的全基因组测序,结合NCBI Refseq数据库中119株B.bifidum基因组进行比较基因组学分析。B.bifidum B1628基因组仅有1条2 234 414 bp的环状染色体且不含质粒,GC含量为62.4%,包含1 769个蛋白质编码区。120株B.bifidum共包含6 554个泛基因,呈开放型。基于987个核心基因构建系统发育树,120株B.bifidum聚为8个不同的分支,呈地区聚集性,B.bifidum B1628属于分支1,该分支菌株均分离自中国。功能分析发现B.bifidum B1628包含叶酸、色氨酸、乳酸合成基因,耐酸、耐胆盐、氧化应激等与环境压力相关基因以及CRISPR-Cas适应性免疫系统。该研究揭示了B.bifidum B1628全基因组特征,发现多个潜在益生基因,为该菌株开发利用及产业化提供数据参考。
The research team isolated Bifidobacterium bifidum B1628 with good acid and bile salt tolerance from the intestine of healthy infants.Heat-killed organisms from this strain can relieve colonic inflammatory edema in inflammatory bowel disease (IBD) mice, which has potential applications.To explore the genetic background of B.bifidum B1628 and the genes with potential probiotic properties, the complete genome of B.bifidum B1628 was sequenced and assembled by combining Illumina and Oxford Nanopore.The genomes of B.bifidum were compared with those of 119 B.bifidum isolates from different countries and regions published by NCBI.The study found that B.bifidum B1628 had only one circular chromosome of 2 234 414 bp and contained no plasmid, with a GC content of 62.4% and 1 769 protein-coding regions.120 strains of B.bifidum contained a total of 6 554 pan genes in an open pattern.A phylogenetic tree was constructed based on the 987 core genes, and the 120 B.bifidum strains were clustered into eight clads with regional aggregation, and B.bifidum B1628 belonged to clade 1, which was isolated from China.Functional annotation showed that B.bifidum B1628 contained genes for folate, tryptophan, and lactate synthesis, genes for acid tolerance, bile salt tolerance, oxidative stress-related genes, and environmental stress-related genes, as well as CRISPR-Cas adaptive immune system.This study presents the genome-wide characterization of B.bifidum B1628 and identifies potential beneficial genes, providing data reference for the development, utilization, and industrialization of this strain.
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