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16S rRNA元编码应用于昆虫产品 (新食品) 的微生物组:对三个参考数据库进行比较分析

Gabriele Spatola¹, Alice Giusti², Laura Gasperetti³

¹Department of Veterinary Sciences, University of Pisa. g.spatola2@studenti.unipi.it.

Italian journal of food safety

|February 24, 2025

概括

选择正确的16S rRNA基因参考数据库会影响食品微生物组分析. SILVA数据库显示,以昆虫为基础的食品的分类学分配率更高,这对于准确的微生物分析至关重要.

科学领域:

微生物学微生物学
生物信息学是一种生物信息学.
食品科学食品科学食品科学

背景情况:

使用下一代测序 (NGS) 的16S rRNA元编码对于食品微生物生物多样性评估至关重要.
生物信息管道需要参考数据库来进行准确的分类学赋值 (顺序,属,物种).
存在多个公共基因组数据库,但它们对食物矩阵的影响尚未完全理解.

研究的目的:

为了调查参考数据库选择如何影响微生物组,以昆虫为基础的食品产品的结果.
确定最合适的参考数据库,以评估这些新型食品来源中的微生物组成.
为了比较SILVA,RDP和NCBI RefSeq数据库的性能.

主要方法:

分析了42种基于昆虫的食品,使用16SrRNA V3-V4区域测序 (Illumina技术).
使用R包"DADA2"进行了生物信息分析.
在SILVA,RDP和NCBI RefSeq数据库中比较了AMPLICON序列变异 (ASV) 赋值百分比和多样性指数.

主要成果:

与RefSeq和RDP相比,SILVA数据库在家族和属级别分配的ASV百分比明显更高.
基于跨数据库的α和β多样性指标,没有观察到微生物组成的显著差异.
确定了121个属,在所有三个数据库中共有56.2%;一些种类是特定于数据库的.

结论:

参考数据库的选择影响了食品微生物组研究中的分类学分配.
在将ASV分配到更高的分类学等级方面,SILVA表现出卓越的表现.
准确的微生物组表征需要更新的参考数据库,以优化新食品中的元编码数据分析.

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