Saroj Dina B, Ahire Jayesh J, Shukla Rohit
Advanced Enzyme Technologies Limited, Sun Magnetica, Louiswadi, Thane-West, Maharashtra 400 604 India.
3 Biotech. 2023 Jul;13(7):238. doi: 10.1007/s13205-023-03662-4. Epub 2023 Jun 16.
In this study, we report on whole genome sequence analysis of clinically documented, commercial probiotic 088AE and genome features contributing to probiotic properties. The whole genome sequence of 088AE generated a single scaffold of 4,598,457 bp with 44.74 mol% G + C. This assembled genome sequence annotated by the RAST resulted in 4371 coding genes, 75 tRNAs, and 22 rRNAs. Gene ontology classification indicated 39.5% proteins with molecular function, 44.24% cellular component, and 16.25% proteins involved in biological processes. In taxonomic analysis, 088AE shared 99% identity with DSM 8716. The gene sequences related to safety and genome stability such as antibiotic resistance (840), virulence factors (706), biogenic amines (1), enterotoxin (0), emetic toxin (0), lanthipeptides (4), prophage (4) and clustered regularly interspaced short palindromic repeats (CRISPR) sequences (11), were identified and evaluated for safety and functions. The absence of functional prophage sequences and the presence of CRISPR indicated an advantage in genome stability. Moreover, the presence of genome features contributing to probiotic characteristics such as acid, and bile salt tolerance, adhesion to the gut mucosa, and environmental resistance ensure the strains survivability when consumed as a probiotic. In conclusion, the absence of risks associated with sequences/genes in the 088AE genome and the presence of essential probiotic traits confirm the strain to be safe for use as a probiotic.
在本研究中，我们报告了临床记录的商业益生菌088AE的全基因组序列分析以及有助于益生菌特性的基因组特征。088AE的全基因组序列产生了一个4,598,457 bp的单支架，G + C含量为44.74 mol%。通过RAST注释的该组装基因组序列产生了4371个编码基因、75个tRNA和22个rRNA。基因本体分类表明，具有分子功能的蛋白质占39.5%，细胞成分占44.24%，参与生物过程的蛋白质占16.25%。在分类分析中，088AE与DSM 8716的同一性为99%。鉴定并评估了与安全性和基因组稳定性相关的基因序列，如抗生素抗性（840个）、毒力因子（706个）、生物胺（1个）、肠毒素（0个）、呕吐毒素（0个）、羊毛硫肽（4个）、前噬菌体（4个）和规律成簇间隔短回文重复序列（CRISPR）（11个）的安全性和功能。功能性前噬菌体序列的缺失和CRISPR的存在表明在基因组稳定性方面具有优势。此外，有助于益生菌特性的基因组特征的存在，如耐酸、耐胆盐、粘附于肠粘膜和环境抗性，确保了该菌株作为益生菌食用时的生存能力。总之，088AE基因组中与序列/基因相关的风险的缺失以及必需益生菌特性的存在证实了该菌株作为益生菌使用是安全的。
