Aziz Tariq, Naveed Muhammad, Shabbir Muhammad Aqib, Sarwar Abid, Naseeb Jasra, Zhao Liqing, Yang Zhennai, Cui Haiying, Lin Lin, Albekairi Thamer H
Department of Food Science and Technology, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, China.
School of Biomedical Engineering, Shenzhen University, Shenzhen, Guangdong, China.
Front Microbiol. 2024 Nov 14;15:1504625. doi: 10.3389/fmicb.2024.1504625. eCollection 2024.
This study investigates the genomic features and probiotic potential of HMX2, isolated from Chinese Sauerkraut, using whole-genome sequencing (WGS) and bioinformatics for the first time. This study also aims to find genetic diversity, antibiotic resistance genes, and functional capabilities to help us better understand its food safety applications and potential as a probiotic. HMX2 was cultured, and DNA was extracted for WGS. Genomic analysis comprised average nucleotide identity (ANI) prediction, genome annotation, pangenome, and synteny analysis. Bioinformatics techniques were used to identify CoDing Sequences (CDSs), transfer RNA (tRNA) and ribosomal RNA (rRNA) genes, and antibiotic resistance genes, as well as to conduct phylogenetic analysis to establish genetic diversity and evolution. The study found a significant genetic similarity (99.17% ANI) between HMX2 and the reference strain. Genome annotation revealed 3,242 coding sequences, 65 tRNA genes, and 16 rRNA genes. Significant genetic variety was found, including 25 antibiotic resistance genes. A phylogenetic study placed HMX2 among closely related bacteria, emphasizing its potential for probiotic and food safety applications. The genomic investigation of showed essential genes, including plnJK and plnEF, which contribute to antibacterial action against foodborne pathogens. Furthermore, genes such as MurA, Alr, and MprF improve food safety and probiotic potential by promoting bacterial survival under stress conditions in food and the gastrointestinal tract. This study introduces the new genomic features of HMX2 about specific genetics and its possibility of relevant uses in food security and technologies. These findings of specific genes involved in antimicrobial activity provide fresh possibilities for exploiting this strain in forming probiotic preparations and food preservation methods. The future research should focus on the experimental validation of antibiotic resistance genes, comparative genomics to investigate functional diversity, and the development of novel antimicrobial therapies that take advantage of 's capabilities.
本研究首次利用全基因组测序（WGS）和生物信息学方法，对从中国酸菜中分离出的HMX2的基因组特征和益生菌潜力进行了研究。本研究还旨在发现其遗传多样性、抗生素抗性基因和功能特性，以帮助我们更好地理解其在食品安全方面的应用以及作为益生菌的潜力。培养了HMX2，并提取DNA用于WGS。基因组分析包括平均核苷酸同一性（ANI）预测、基因组注释、泛基因组和共线性分析。利用生物信息学技术鉴定编码序列（CDS）、转运RNA（tRNA）和核糖体RNA（rRNA）基因以及抗生素抗性基因，并进行系统发育分析以确定遗传多样性和进化关系。研究发现HMX2与参考菌株之间存在显著的遗传相似性（ANI为99.17%）。基因组注释显示有3242个编码序列、65个tRNA基因和16个rRNA基因。发现了显著的遗传多样性，包括25个抗生素抗性基因。系统发育研究将HMX2置于密切相关的细菌之中，突出了其在益生菌和食品安全应用方面的潜力。对HMX2的基因组研究显示了一些关键基因，包括plnJK和plnEF，它们有助于对食源性病原体产生抗菌作用。此外，MurA、Alr和MprF等基因通过促进细菌在食物和胃肠道应激条件下的存活，提高了食品安全和益生菌潜力。本研究介绍了HMX2在特定遗传学方面的新基因组特征及其在食品安全和技术方面相关应用的可能性。这些涉及抗菌活性的特定基因的发现为利用该菌株开发益生菌制剂和食品保存方法提供了新的可能性。未来的研究应侧重于抗生素抗性基因的实验验证、比较基因组学以研究功能多样性，以及开发利用HMX2能力的新型抗菌疗法。
