Bloomfield Samuel J, Hildebrand Falk, Zomer Aldert L, Palau Raphaëlle, Mather Alison E
Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
Centre for Microbial Interactions, Norwich Research Park, Norwich, UK.
Microb Genom. 2025 Jan;11(1). doi: 10.1099/mgen.0.001337.
A diverse array of micro-organisms can be found on food, including those that are pathogenic or resistant to antimicrobial drugs. Metagenomics involves extracting and sequencing the DNA of all micro-organisms on a sample, and here, we used a combination of culture and culture-independent approaches to investigate the microbial ecology of food to assess the potential application of metagenomics for the microbial surveillance of food. We cultured common foodborne pathogens and other organisms including , spp., spp. and spp. from five different food commodities and compared their genomes to the microbial communities obtained by metagenomic sequencing following host (food) DNA depletion. The microbial populations of retail food were found to be predominated by psychrotrophic bacteria, driven by the cool temperatures in which the food products are stored. Pathogens accounted for a small percentage of the food metagenome compared to the psychrotrophic bacteria, and cultured pathogens were inconsistently identified in the metagenome data. The microbial composition of food varied amongst different commodities, and metagenomics was able to classify the taxonomic origin of 59% of antimicrobial resistance genes (ARGs) found on food to the genus level, but it was unclear what percentage of ARGs were associated with mobile genetic elements and thus transferable to other bacteria. Metagenomics may be used to survey the ARG burden, composition and carriage on foods to which consumers are exposed. However, food metagenomics, even after depleting host DNA, inconsistently identifies pathogens without enrichment or further bait capture.
在食物上可以发现各种各样的微生物，包括那些致病的或对抗菌药物有抗性的微生物。宏基因组学涉及提取样本中所有微生物的DNA并进行测序，在此，我们结合了培养法和非培养法来研究食物的微生物生态学，以评估宏基因组学在食物微生物监测中的潜在应用。我们从五种不同的食品中培养了常见的食源性病原体和其他微生物，包括 菌属、 菌属、 菌属和 菌属，并将它们的基因组与宿主（食物）DNA去除后通过宏基因组测序获得的微生物群落进行比较。发现零售食品中的微生物种群以嗜冷菌为主，这是由食品储存的低温环境所驱动的。与嗜冷菌相比，病原体在食物宏基因组中所占比例较小，并且在宏基因组数据中培养出的病原体识别结果并不一致。不同食品的微生物组成各不相同，宏基因组学能够将在食物上发现的59%的抗微生物药物抗性基因（ARGs）的分类学来源归类到属水平，但尚不清楚有多少比例的ARGs与可移动遗传元件相关，从而可转移到其他细菌中。宏基因组学可用于调查消费者接触的食品上的ARGs负担、组成和携带情况。然而，即使去除宿主DNA后，食物宏基因组学在没有富集或进一步诱饵捕获的情况下，对病原体的识别也不一致。
