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    • Improved Sampling and DNA Extraction Procedures for Microbiome Analysis in Food-Processing Environments

    Nature Protocols（2024）

    Univ Leon | Department of Agricultural Sciences | Teagasc Food Research Centre | QIAGEN GmbH | Department of Cellular | Spanish Natl Res Council IPLA CSIC | Austrian Competence Centre for Feed and Food Quality | Univ Vet Med Vienna | Microbiology Research Group

    Cited 4|Views7
    Abstract
    Deep investigation of the microbiome of food-production and food-processing environments through whole-metagenome sequencing (WMS) can provide detailed information on the taxonomic composition and functional potential of the microbial communities that inhabit them, with huge potential benefits for environmental monitoring programs. However, certain technical challenges jeopardize the application of WMS technologies with this aim, with the most relevant one being the recovery of a sufficient amount of DNA from the frequently low-biomass samples collected from the equipment, tools and surfaces of food-processing plants. Here, we present the first complete workflow, with optimized DNA-purification methodology, to obtain high-quality WMS sequencing results from samples taken from food-production and food-processing environments and reconstruct metagenome assembled genomes (MAGs). The protocol can yield DNA loads >10 ng in >98% of samples and >500 ng in 57.1% of samples and allows the collection of, on average, 12.2 MAGs per sample (with up to 62 MAGs in a single sample) in ~1 week, including both laboratory and computational work. This markedly improves on results previously obtained in studies performing WMS of processing environments and using other protocols not specifically developed to sequence these types of sample, in which <2 MAGs per sample were obtained. The full protocol has been developed and applied in the framework of the European Union project MASTER (Microbiome applications for sustainable food systems through technologies and enterprise) in 114 food-processing facilities from different production sectors.
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    【要点】：本研究提出了一种优化的DNA提取流程，用于从食品加工环境中低生物量样本获取高质量的全基因组测序结果，显著提高了微生物组组装基因组数量。
    

    【方法】：研究采用了一种改进的DNA纯化方法，包括优化的采样和DNA提取步骤，以适应食品生产与加工环境中低生物量样本的DNA提取。
    

    【实验】：在欧盟项目MASTER框架下，该流程被应用于114个不同生产部门的食品加工设施中，实验结果表明，该流程在超过98%的样本中可获得超过10 ng的DNA负载，在57.1%的样本中获得超过500 ng的DNA负载，平均每个样本可收集12.2个微生物组装基因组（单个样本最多可达62个），包括实验室和计算工作在内仅需约1周时间。