【摘要】 益生菌是一类有益于人体健康的微生物,主要包括细菌和真菌.益生菌的鉴定一直是学界亟需解决的技术问题,传统的分类学方法只能做种属水平的鉴定,而基于基因组学分析可鉴定到种或株水平.本研究对公共数据库中记载的我国《可用于食品的菌种名单》中的16种乳酸杆菌和5种双歧杆菌的基因组数据进行了全基因组比对分析,并应用核心基因平均核苷酸相似性(core genes average nucleotide identity, cANI)进行了物种的重新分类和鉴定方法探索.结果显示,乳酸杆菌和双歧杆菌的cANI值具有种属特异性,其中乳酸杆菌的cANI值在93.6%～99.6%之间,双歧杆菌的c ANI值在94.9%～98.1%之间,同时发现25株乳酸杆菌和1株两歧双歧杆菌有分类学错误.对247株乳酸杆菌和113株双歧杆菌基因组完成图的比对分析结果显示,乳酸杆菌和双歧杆菌菌株间的差异基因数目最多可达436个,菌株间的cANI相似值最小可达1个单核苷酸多态性(single nucleotide polymorphism, SNP).针对乳酸杆菌和双歧杆菌的毒力基因和耐药基因分析显示,在目前用于食品生产的菌株中均未发现毒力相关基因,同时发现有20%以上的菌株携带不同种类的耐药基因.结论:乳酸杆菌和双歧杆菌不同种的cANI值差异较大,有种属特异性,可用于益生菌的种属鉴定;同一物种不同菌株间的基因和SNP数目差异可用于菌株鉴定.更多还原

【Abstract】 Probiotics are beneficial microorganisms for human health, including bacteria and fungi. The identification of probiotics has always been a pressing technical issue in the academic community. Traditional taxonomic methods can only identify at the species level,while genomic analysis can identify at the strain or species level. In this study, a whole-genome comparison analysis was performed on 16 strains of lactobacilli and 5 strains of Bifidobacterium listed in China’s “List of Microorganisms Used in Food”. The core genes average nucleotide identity(cANI) was applied to explore the method of reclassification and identification of species. The results showed that the cANI values of lactobacilli and Bifidobacterium had species-specificity, with cANI values of lactobacilli ranging from 93.6% to 99.6% and cANI values of Bifidobacterium ranging from 94.9% to 98.1%. At the same time, 25 strains of lactobacilli and one strain of Bifidobacterium were found to have taxonomic errors. The results of comparative genome analysis of 247 strains of lactobacilli and 113 strains of Bifidobacterium showed that the number of different genes between strains of lactobacilli and Bifidobacterium could reach up to 436, and the minimum c ANI similarity value between strains was 1 single nucleotide polymorphisms(SNPs). The analysis of virulence genes and resistance genes in lactobacilli and Bifidobacterium showed that no virulence-related genes were found in all commercial strains, and more than 20% of strains carried different types of resistance genes.In conclusion, the cANI values of different species of lactobacilli and Bifidobacterium have significant differences and species specificity, which can be used for the identification of probiotic species, and the differences in gene and SNP numbers between different strains of the same species can be used for strain identification.更多还原