Ready-to-eat fast food vending outlets provide a cheap and readily available food. Foodborne diseases have been previously reported in Embu, Kenya, but data on the prokaryotic metagenome in vended foods is scanty. This study aimed to determine the prokaryotic diversity in fruits, vegetable salad, African sausage, chips (potato fries), fried fish, roasted beef (meat), smokies, samosa, soil, and water collected from food vendors and the surrounding environment in Embu Town and Kangaru Market. The study used 454 pyrosequencing, Illumina high-throughput sequencing of 16S rRNA gene in the analysis of total community DNA extracted from samples using the phenol-chloroform method. The 16S rRNA gene variable region (V4-V7) of the extracted DNA was amplified and library construction performed. Sequence analysis was done using QIIME2. Hierarchical clustering of samples, diversity indices, rarefaction curves, and Venn diagrams were generated using the R programming language in R software version 3.6.3. Bacterial operational taxonomic units (OUTs) were distributed in Proteobacteria (52.81%), Firmicutes (31.16%), and Lentisphaerae (0.001%). The OTUs among archaea were Candidatus Nitrososphaera (63.56%) and Nitrososphaera spp. (8.77%). Brucella spp. and Bacillus cereus associated with foodborne diseases were detected. Potential pathogens, Rickettsia spp. in risk group 2 and Brucella spp. in risk group 3, were detected. Uncultured Candidatus Koribacter and Candidatus Solibacter were also detected in the food samples. There was a significant difference in the microbial community structure among the sample types (P<0.1). The results demonstrated the presence of some prokaryotes that are associated with food spoilage or foodborne diseases in vended foods and environmental samples. This study also detected uncultured prokaryotes. The presence of potential pathogens calls for stringent hygiene measures in food vending operations.

中文翻译：

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出售食品和环境样品中的原核多样性和潜在致病菌

即食快餐自动售货机提供便宜且容易获得的食物。肯尼亚恩布此前曾报道过食源性疾病，但关于出售食品中原核宏基因组的数据很少。本研究旨在确定从食品供应商和 Embu 周边环境收集的水果、蔬菜沙拉、非洲香肠、薯条（薯条）、炸鱼、烤牛肉（肉）、烟熏、萨摩萨、土壤和水的原核多样性镇和袋鼠市场。该研究使用 454 焦磷酸测序，Illumina 对 16S rRNA 基因进行高通量测序，对使用苯酚-氯仿法从样品中提取的总群落 DNA 进行分析。对提取的DNA的16S rRNA基因可变区（V4-V7）进行扩增并进行文库构建。使用QIIME2进行序列分析。样本的层次聚类、多样性指数、稀疏曲线和维恩图是使用 R 软件版本 3.6.3 中的 R 编程语言生成的。细菌操作分类单位 (OUTs) 分布在变形菌门 (52.81%)、厚壁菌门 (31.16%) 和 Lentisphaerae (0.001%) 中。古细菌中的 OTU 为 Candidatus Nitrososphaera (63.56%) 和 Nitrososphaera spp。(8.77%)。布鲁氏菌属 检出与食源性疾病有关的蜡样芽孢杆菌。潜在病原体，立克次体。在风险组 2 和布鲁氏菌属中。在风险组 3 中，检测到。在食物样本中亦检出未培养的念珠菌属 Koribacter 及念珠菌属 Solibacter。样品类型间微生物群落结构存在显着差异（P<0.1）。结果表明，在出售的食品和环境样品中存在一些与食品腐败或食源性疾病相关的原核生物。该研究还检测到未培养的原核生物。潜在病原体的存在要求在食品自动售货业务中采取严格的卫生措施。