Abstract：
BACKGROUND: Lactiplantibacillus plantarum 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.
METHODS: L. plantarum 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.
RESULTS: The 3.4 Mb genome of L. plantarum 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.
CONCLUSIONS: 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 in vitro and in vivo studies are warranted to validate the functional attributes and probiotic potential of L. plantarum 12-3. Expanding the scope of the research to encompass a broader range of L. plantarum 12-3 strains and comparative analyses with other probiotic species would enhance our understanding of this organism\'s genetic diversity and functional properties.
METHODS: L. plantarum 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.
RESULTS: The 3.4 Mb genome of L. plantarum 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.
CONCLUSIONS: 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 in vitro and in vivo studies are warranted to validate the functional attributes and probiotic potential of L. plantarum 12-3. Expanding the scope of the research to encompass a broader range of L. plantarum 12-3 strains and comparative analyses with other probiotic species would enhance our understanding of this organism\'s genetic diversity and functional properties.
摘要：
背景：植物乳杆菌12-3作为益生菌菌株具有很大的希望，然而，它的全部潜力仍未开发。这项研究旨在通过探索其基因组景观来更好地了解这种潜在的治疗菌株，遗传多样性,CRISPR-Cas机制，基因型，以及益生菌功能和安全应用的机械观点。
方法：L.从西藏开菲尔谷物中分离出12-3的植物，随后,Illumina和单分子实时（SMRT）技术用于从该生物体中提取和测序基因组DNA。在进行了全基因组和系统发育分析后，使用平均核苷酸同一性(ANI)来确认菌株的分类学同一性。使用综合抗生素抗性数据库(CARD)进行抗生素抗性基因分析。抗菌药物敏感性试验,和毒力基因鉴定也包括在我们的基因组分析中，以评估食品安全。前噬菌体，基因组岛，插入序列,还进行了CRISPR-Cas序列分析，以深入了解细菌基因组中的遗传成分和防御机制。
结果：植物乳杆菌12-3的3.4Mb基因组组装具有99.1％的完整性和低污染。使用基因预测工具共发现3234个具有正常长度和基因间间距的基因。泛基因组研究证明了基因多样性并提供了功能注释，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抗生素耐药性的概况，这有利于用作益生菌。插入序列的分析，基因组岛，和基因组内的预言提供了有关遗传成分及其对进化的可能影响的信息。
结论：本研究中发现的关键遗传元件在细菌防御机制中起着至关重要的作用，并为未来的基因组工程工作提供了有趣的前景。此外，我们的研究结果表明，进一步的体外和体内研究有必要验证植物乳杆菌12-3的功能属性和益生菌潜力。扩大研究范围以涵盖更广泛的植物乳杆菌12-3菌株和与其他益生菌物种的比较分析将增强我们对该生物的遗传多样性和功能特性的理解。
方法：L.从西藏开菲尔谷物中分离出12-3的植物，随后,Illumina和单分子实时（SMRT）技术用于从该生物体中提取和测序基因组DNA。在进行了全基因组和系统发育分析后，使用平均核苷酸同一性(ANI)来确认菌株的分类学同一性。使用综合抗生素抗性数据库(CARD)进行抗生素抗性基因分析。抗菌药物敏感性试验,和毒力基因鉴定也包括在我们的基因组分析中，以评估食品安全。前噬菌体，基因组岛，插入序列,还进行了CRISPR-Cas序列分析，以深入了解细菌基因组中的遗传成分和防御机制。
结果：植物乳杆菌12-3的3.4Mb基因组组装具有99.1％的完整性和低污染。使用基因预测工具共发现3234个具有正常长度和基因间间距的基因。泛基因组研究证明了基因多样性并提供了功能注释，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抗生素耐药性的概况，这有利于用作益生菌。插入序列的分析，基因组岛，和基因组内的预言提供了有关遗传成分及其对进化的可能影响的信息。
结论：本研究中发现的关键遗传元件在细菌防御机制中起着至关重要的作用，并为未来的基因组工程工作提供了有趣的前景。此外，我们的研究结果表明，进一步的体外和体内研究有必要验证植物乳杆菌12-3的功能属性和益生菌潜力。扩大研究范围以涵盖更广泛的植物乳杆菌12-3菌株和与其他益生菌物种的比较分析将增强我们对该生物的遗传多样性和功能特性的理解。
