Genomic Investigation of a Bacillus subtilis Strain Sourced from Commercially Available Milk Powder in China Reveals Potential Risk Factors.

IF 2.9 3区医学 Q2 INFECTIOUS DISEASES

Infection and Drug Resistance Pub Date : 2025-08-25 eCollection Date: 2025-01-01 DOI:10.2147/IDR.S544153

Ling Zhu, Keyu Chen, Liu Xu, Afeng Wang, Haojian Gan, Junhong Sun, Yujie Wu, Yutong Li, Yingying Guo, Yanfeng Yi, Xinhua Qiang, Jie He, Hongchang Zhou, Yibin Lin

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Abstract

Background: Milk powder is a key food source, especially for infants and vulnerable groups. However, Bacillus contamination during production, storage, or handling can cause spoilage, quality issues, or health risks. This study identified and isolated Bacillus subtilis from commercially available Chinese milk powder.

Methods: A pure colony of Bacillus subtilis was isolated from an LB agar plate supplemented with milk powder and identified using mass spectrometry. The genome of this strain was sequenced using third-generation sequencing technology. Following assembly, the genome was functionally annotated and subjected to comprehensive bioinformatic analysis.

Results: Genomic analysis classified the strain as Bacillus subtilis via MALDI-TOF and ANI (98.82% with B. subtilis AMR1). Its genome features a 4.26 Mbp chromosome and 97.6 kbp plasmid encoding 4,539 genes, including virulence factors (209 genes), antibiotic resistance genes (19 genes), and carbohydrate-active enzymes (253 genes). Key virulence mechanisms include immune modulation, stress adaptation, toxin production, and biofilm formation. Antibiotic resistance involves efflux pumps (eg, qacJ, bmr), enzymatic inactivation (eg, FosBx1, aadK), and target modification (eg, vanG cluster, tet(45)). Phylogenetically (LIN78), the strain clusters with foodborne B. subtilis isolates (eg, from Korean gochujang and soybean), diverging from B. cereus and environmental Bacillus clades. Comparative genomics revealed 53 LIN78-specific genes, encompassing defense mechanisms and mobile elements, and synteny in all homologs except B. subtilis ATCC 11774. Genomic islands, CRISPR arrays, and recombination-associated repeats indicate adaptive evolution.

Conclusion: This study characterizes Bacillus subtilis LIN78, a genomically plastic strain isolated from Chinese milk powder. It exhibits adaptation to food environments via horizontal gene transfer, stress tolerance, and spoilage traits, while carrying antimicrobial resistance risks and potential biotechnological applications. The findings necessitate genomic monitoring to manage food safety, resistance spread, and leverage its dual role as both a spoilage organism and source of bioactive compounds..

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一株来自中国市售奶粉的枯草芽孢杆菌的基因组研究揭示了潜在的危险因素。

背景：奶粉是一种重要的食物来源，尤其是对婴儿和弱势群体。然而，在生产、储存或处理过程中，芽孢杆菌污染会导致腐败、质量问题或健康风险。本研究从市售奶粉中分离鉴定枯草芽孢杆菌。方法：从添加奶粉的LB琼脂平板上分离到枯草芽孢杆菌，并用质谱法对其进行鉴定。采用第三代测序技术对该菌株进行基因组测序。组装后，对基因组进行功能注释并进行全面的生物信息学分析。结果：基因组分析通过MALDI-TOF和ANI鉴定菌株为枯草芽孢杆菌（98.82%为枯草芽孢杆菌AMR1）。其基因组具有一条4.26 Mbp的染色体和97.6 kbp的质粒，编码4,539个基因，包括毒力因子（209个基因）、抗生素抗性基因（19个基因）和碳水化合物活性酶（253个基因）。关键的毒力机制包括免疫调节、应激适应、毒素产生和生物膜形成。抗生素耐药性包括外排泵（如qacJ、bmr）、酶失活（如FosBx1、aadK）和靶标修饰（如vanG簇、tet(45)）。系统发育（LIN78），该菌株与食源性枯草芽孢杆菌分离株（例如，来自韩国辣酱和大豆）聚集在一起，从蜡样芽孢杆菌和环境芽孢杆菌分支中分化出来。比较基因组学揭示了53个lin78特异性基因，包括防御机制和移动元件，并在除枯草芽孢杆菌ATCC 11774外的所有同源物中具有一致性。基因组岛、CRISPR阵列和重组相关重复序列表明适应性进化。结论：从中国奶粉中分离到一株具有基因组可塑性的枯草芽孢杆菌LIN78。它通过水平基因转移、抗逆性和腐败特性表现出对食物环境的适应性，同时具有抗菌素耐药性风险和潜在的生物技术应用。这些发现需要基因组监测来管理食品安全、耐药性传播，并利用其作为腐败生物体和生物活性化合物来源的双重作用。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Infection and Drug Resistance Medicine-Pharmacology (medical)

CiteScore

5.60

自引率

7.70%

发文量

826

审稿时长

16 weeks

期刊介绍： About Journal Editors Peer Reviewers Articles Article Publishing Charges Aims and Scope Call For Papers ISSN: 1178-6973 Editor-in-Chief: Professor Suresh Antony An international, peer-reviewed, open access journal that focuses on the optimal treatment of infection (bacterial, fungal and viral) and the development and institution of preventative strategies to minimize the development and spread of resistance.