Bukhari Sayyad Ali Raza, Irfan Muhammad, Ahmad Irfan, Chen Lijing
Department of Biotechnology, University of Sargodha, Sargodha 40100, Pakistan.
Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 61421, Saudi Arabia.
Microorganisms. 2022 Jul 4;10(7):1350. doi: 10.3390/microorganisms10071350.
imparts important health benefits and is considered a next-generation probiotic. It is imperative to understand the genomic diversity and metabolic potential of the species for safer applications as probiotics. As it resides with both health-promoting and pathogenic bacteria, understanding the evolutionary patterns are crucial, but this area remains largely unexplored. Moreover, pan-genome has previously been established based on only a limited number of strains and without careful strain selection. The pan-genomics have become very important for understanding species diversity and evolution. In the current study, a systematic approach was used to find a refined pan-genome profile of by excluding too-diverse strains based on average nucleotide identity-based species demarcation. The strains were divided into four phylogroups using a variety of clustering techniques. Horizontal gene transfer and recombination patterns were also elucidated. Evolutionary patterns revealed that different phylogroups were expanding differently. Furthermore, a comparative evaluation of the metabolic potential of the pan-genome and its subsections was performed. Lastly, the study combines functional annotation, persistent genome, and essential genes to devise an approach to determine a minimal genome that can systematically remove unwanted genes, including virulent factors. The selection of one strain to be used as a chassis for the prediction of a reduced genome was very carefully performed by analyzing several genomic parameters, including the number of unique genes and the resistance and pathogenic potential of the strains. The strategy could be applied to other microbes, including human-associated microbiota, towards a common goal of predicting a minimal or a reduced genome.
具有重要的健康益处，被认为是一种下一代益生菌。为了更安全地将其作为益生菌应用，了解该物种的基因组多样性和代谢潜力至关重要。由于它与促进健康的细菌和致病细菌共存，了解其进化模式至关重要，但这一领域在很大程度上仍未得到探索。此外，之前的泛基因组仅基于有限数量的菌株建立，且没有进行仔细的菌株选择。泛基因组学对于理解物种多样性和进化变得非常重要。在当前的研究中，采用了一种系统的方法，通过基于平均核苷酸同一性的物种划分排除差异过大的菌株，来找到一个经过优化的泛基因组图谱。使用多种聚类技术将菌株分为四个系统发育组。还阐明了水平基因转移和重组模式。进化模式表明不同的系统发育组以不同的方式扩展。此外，对泛基因组及其子部分的代谢潜力进行了比较评估。最后，该研究结合功能注释、持久基因组和必需基因，设计了一种方法来确定一个最小基因组，该基因组可以系统地去除不需要的基因，包括毒力因子。通过分析几个基因组参数，包括独特基因的数量以及菌株的抗性和致病潜力，非常仔细地选择了一个菌株作为预测简化基因组的底盘。该策略可应用于其他微生物，包括与人类相关的微生物群，以实现预测最小或简化基因组的共同目标。
