Tracking the microbiota of five vegetables from farm to retail distribution in Dakar using 16S rRNA sequencing

Foodborne illnesses are generally caused by the lack of hygiene in consumed food. In Senegal, particularly in Dakar, mixed salads are served daily in restaurants and have been identified as a source of numerous food poisoning cases. Therefore, in this study, we focused on monitoring the microbiota of five commonly raw-consumed salad vegetables (celery, cabbage, lettuce, bell pepper, and tomato), from the fields where they are cultivated to the markets and supermarkets where they are distributed. We aimed to assess the impact of the distribution areas whether suburban or urban on the microbiota of these vegetables. Samples were collected at multiple stages along the distribution chain in both urban and peri-urban environments. Microbial characterization was conducted using 16S rRNA gene sequencing, with bioinformatic analysis performed using Kraken2, a high-performance taxonomic classifier based on NCBI databases.

Three key microbial parameters were assessed: Alpha diversity (richness, Shannon, Simpson, Pielou indices), Beta diversity (NMDS ordination), Relative abundance of dominant bacterial genera.

Vegetables collected directly from farms exhibited the highest bacterial richness, reflecting environmental exposure, yet displayed low community balance, with dominance by genera such as Glutamicibacter (~34 %), Xanthomonas (~34 %), Pseudomonas (~34 %) and Sodalis. Suburban market vegetables showed intermediate richness but better taxonomic balance, often dominated by Acinetobacter (~80 %), or Weissella. (~20 %) and the same goes for Urban market Weissella (~60 %), Sodalis (~20 %). Suburban Supermarket samples exhibited the lowest diversity Exiguobacterium (~40 %), others genres (~20 %), and in Urban Supermarket Xanthomonas (~65 %), Acinetobacter (~35 %) likely due to post-harvest processing (e.g., washing, refrigeration), and showed more homogeneous microbial communities. Beta diversity analysis revealed distinct clustering by environment type: field samples were highly variable, while market and supermarket samples were more similar, suggesting standardized post-harvest handling or shared sources of contamination. This study highlights the significant impact of the distribution environment on the microbiota of raw vegetables in Dakar and underscores the need to improve post-harvest practices to ensure food safety and microbial quality in urban food systems.

Keywords : Vegetables, microbiota, 16S metagenomics, food hygiene, distribution chain.