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.

通过全宏基因组测序（WMS）对食品生产和食品加工环境中的微生物组进行深入研究，可以提供有关其中微生物群落的分类组成和功能潜力的详细信息，这对环境监测项目具有巨大的潜在好处。然而，某些技术挑战危及 WMS 技术实现这一目标的应用，其中最相关的挑战是从食品加工厂的设备、工具和表面收集的经常低生物量的样品中回收足够量的 DNA。在这里，我们提出了第一个完整的工作流程，采用优化的 DNA 纯化方法，从食品生产和食品加工环境中采集的样本获得高质量的 WMS 测序结果，并重建宏基因组组装基因组 (MAG)。该方案可在 >98% 的样品中产生 >10 ng 的 DNA 载量，在 57.1% 的样品中产生 >500 ng 的 DNA 载量，并允许在 ~ 时间内收集每个样品平均 12.2 MAG（单个样品中最多 62 MAG）。 1 周，包括实验室和计算工作。这显着改善了之前在对处理环境进行 WMS 的研究中获得的结果，并使用其他未专门开发的协议来对这些类型的样本进行测序，其中每个样本获得 <2 MAG。完整的协议已在欧盟 MASTER 项目（通过技术和企业实现可持续食品系统的微生物组应用）框架内制定并应用于来自不同生产部门的 114 个食品加工设施。