Gut and blood microbiota of Nile tilapia (Oreochromis niloticus) reared with lettuce (Lactuca sativa) and challenged with Escherichia coli and Vibrio cholerae in aquaponic systems

Aquaponics, a bio-integrated system that combines fish farming and vegetable cultivation, has gained significant attention due to its rapid expansion and potential for sustainable food production. In aquaponics, along with plants and fish, both beneficial and harmful microorganisms are also present. This study was conducted to assess the microbiota diversity of Nile tilapia reared with lettuce in aquaponic systems, with a focus on food safety implications. A total of 144 Nile tilapia juveniles with an average initial weight of 30.7 ± 0.03 g were randomly stocked and allocated to three treatments, each with three replicates. In treatment one, the fish were not challenged with any pathogenic bacteria, while in treatments two and three, they were challenged with Escherichia coli (ATCC 8739) and Vibrio cholerae (ATCC 9458), respectively. Faecal and blood samples were collected before and after challenging Nile tilapia. The diversity of microbial communities was assessed by sequencing the V1-V3 regions of the 16S rRNA gene using Illumina NextSeq2000. In total, 216 amplicon sequence variants were identified in faecal samples and 162 in blood samples, all belonging to the bacteria kingdom. Taxonomic analysis demonstrates that multiple detected genera encompass species with known pathogenicity to humans and documented association with foodborne illnesses and mortality. These included Agrobacterium, Streptococcus, Klebsiella, Clostridium, Brucella, Plesiomanas, Edwardsiella, Aeromonas, and Bacillus. The findings highlight the importance of incorporating public health considerations within an aquaponic system in which vegetables are grown together with fish, in order to reduce the risks of contamination and enhance food safety.