Key Laboratory of Geriatric Nutrition and Health of Ministry of Education, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, 100048 Beijing, China.
Department of Biotechnology, Faculty of Science & Technology, University of Central Punjab, 54590 Lahore, Pakistan.
Front Biosci (Landmark Ed). 2024 Apr 11;29(4):147. doi: 10.31083/j.fbl2904147.
12-3 holds great promise as a probiotic bacterial strain, yet its full potential remains untapped. This study aimed to better understand this potential therapeutic strain by exploring its genomic landscape, genetic diversity, CRISPR-Cas mechanism, genotype, and mechanistic perspectives for probiotic functionality and safety applications.
12-3 was isolated from Tibetan kefir grains and, subsequently, Illumina and Single Molecule Real-Time (SMRT) technologies were used to extract and sequence genomic DNA from this organism. After performing pan-genomic and phylogenetic analysis, Average Nucleotide Identity (ANI) was used to confirm the taxonomic identity of the strain. Antibiotic resistance gene analysis was conducted using the Comprehensive Antibiotic Resistance Database (CARD). Antimicrobial susceptibility testing, and virulence gene identification were also included in our genomic analysis to evaluate food safety. Prophage, genomic islands, insertion sequences, and CRISPR-Cas sequence analyses were also carried out to gain insight into genetic components and defensive mechanisms within the bacterial genome.
The 3.4 Mb genome of 12-3, was assembled with 99.1% completeness and low contamination. A total of 3234 genes with normal length and intergenic spacing were found using gene prediction tools. Pan-genomic studies demonstrated gene diversity and provided functional annotation, whereas phylogenetic analysis verified taxonomic identity. Our food safety study revealed a profile of antibiotic resistance that is favorable for use as a probiotic. Analysis of insertional sequences, genomic islands, and prophage within the genome provided information regarding genetic components and their possible effects on evolution.
Pivotal genetic elements uncovered in this study play a crucial role in bacterial defense mechanisms and offer intriguing prospects for future genome engineering efforts. Moreover, our findings suggest further and studies are warranted to validate the functional attributes and probiotic potential of 12-3. Expanding the scope of the research to encompass a broader range of 12-3 strains and comparative analyses with other probiotic species would enhance our understanding of this organism's genetic diversity and functional properties.
12-3 作为一种益生菌菌株具有巨大的潜力，但它的全部潜力尚未被开发。本研究旨在通过探索其基因组景观、遗传多样性、CRISPR-Cas 机制、基因型和益生菌功能和安全性应用的机制观点，更好地了解这种有潜力的治疗菌株。
12-3 是从西藏开菲尔粒中分离出来的，随后使用 Illumina 和单分子实时 (SMRT) 技术从该生物中提取和测序基因组 DNA。在进行全基因组和系统发育分析后，使用平均核苷酸同一性 (ANI) 确认菌株的分类学身份。使用综合抗生素抗性数据库 (CARD) 进行抗生素抗性基因分析。还包括抗菌药物敏感性测试和毒力基因鉴定，以评估食品安全。对噬菌体、基因组岛、插入序列和 CRISPR-Cas 序列进行分析，以深入了解细菌基因组中的遗传成分和防御机制。
12-3 的 3.4 Mb 基因组，组装完整性为 99.1%，污染程度低。使用基因预测工具发现了总共 3234 个具有正常长度和基因间间距的基因。全基因组研究表明基因多样性，并提供功能注释，而系统发育分析验证了分类学身份。我们的食品安全研究揭示了一种有利于用作益生菌的抗生素耐药谱。对基因组中插入序列、基因组岛和噬菌体的分析提供了有关遗传成分及其对进化可能影响的信息。
本研究中揭示的关键遗传元件在细菌防御机制中发挥着至关重要的作用，并为未来的基因组工程努力提供了有趣的前景。此外，我们的发现表明需要进一步和研究来验证 12-3 的功能属性和益生菌潜力。将研究范围扩大到涵盖更广泛的 12-3 菌株，并与其他益生菌物种进行比较分析，将增强我们对该生物遗传多样性和功能特性的理解。
