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Purpose 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. Methods 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. Results 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&lt;0.1). Conclusion 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.

Prokaryotic diversity and potentially pathogenic bacteria in vended foods and environmental samples