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Updated: Jun 5, 2025

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基因提取,PCR放大,测序和生物信息分析对使用PacBio长时间读取的amplicon测序的食品相关模拟社区的影响
Mareike Baer1, Lisa Höppe2, Waldemar Seel3
1Institute of Nutritional and Food Sciences, Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, 53115, Bonn, Germany. mabaer@uni-bonn.de.
BMC microbiology
|December 6, 2024
概括
长读测序准确地描述了食品微生物组,但PCR放大引入了偏差. 与模拟社区进行基准测试对于可靠的食品微生物组分析和风险评估至关重要.
科学领域:
- 微生物学 微生物学
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 长期阅读的16S rRNA基因测序为食品微生物群的表征提供了很高的潜力.
- 全长基因测序使得物种层面的分类学解析成为可能.
- 挑战包括不同丰度,属内差异化和新物种检测.
研究的目的:
- 用模拟社区对与食物相关的微生物组进行长时间读数测序的基准测试.
- 研究DNA提取,PCR,测序和生物信息学对结果的影响.
- 评估可靠地表征食品微生物群的方法.
主要方法:
- 使用模拟社区的挤奶机生物膜和生肉.
- 对比DNA提取套件,PCR放大和测序.
- 评估生物信息学分析,包括参考数据库和规范化.
主要成果:
- 通过自定义的RefSeq数据库,PacBio CCS读取实现了正确的分类学赋值.
- PCR放大引入了与G+C含量相关的显著偏差.
- 精确复制社区组成的测序;数据库选择影响了新物种的识别.
结论:
- 与特定息地模拟社区进行基准测试对于方法评估至关重要.
- 长读数测序为深入的微生物组表征提供了卓越的物种级别分辨率.
- 精确的物种识别通过区分致病菌和非致病菌株来改善食品安全风险评估.
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