Metagenomic analysis of the tomato microbiome in Colombia reveals bacterial diversity, potential pathogens, and resistance determinants

Tomato ( Solanum lycopersicum ), a globally consumed crop, can act as a reservoir of microorganisms with potential food safety implications. This study aimed to characterize the bacterial diversity associated with Colombian tomato crops and to identify pathogenic and resistant bacteria in fruits. Rhizospheric soil, irrigation water, and tomato fruit samples were analyzed using 16S rRNA gene sequencing and shotgun metagenomics for the recovery of metagenome-assembled genomes (MAGs) from the fruits. The phyla Proteobacteria, Bacteroidota, Firmicutes, and Actinobacteriota predominated in all three compartments. Soil and water harbored potential human pathogens, including Escherichia-Shigella and Pseudomonas . Soil contained a vast reservoir of 318 bacterial genera, while only 35 genera established within fruits, dominated by Erwinia , Weissella , and Leuconostoc . This strong ecological filtering retained taxa of concern for public health. MAGs from fruit endophytes revealed a notable repertoire of virulence and resistance genes. Hemolysin toxins ( tlyC , hlyIII ) were detected in 87.5% of MAGs, supporting their pathogenic potential. Clinically relevant antibiotic resistance determinants were also identified, including vanX (vancomycin resistance) in Weissella and Leuconostoc , and multiple tet genes (tetracycline resistance) in Lactococcus . The presence of these genes directly in edible tissues highlights the potential risk of transferring resistant and potentially virulent bacteria to consumers. These findings suggest that Colombian tomatoes internalize microorganisms from contaminated environments, creating a direct link between agricultural practices and foodborne risks. Such vulnerabilities in the production chain underscore the urgent need for proactive monitoring and mitigation strategies to ensure food safety from farm to market. • Tomato microbiome shows key functions and genes with pathogenic potential. • Presence of clinically relevant genera in tomato suggests potential pathogen transfer. • Virulence genes in Weissella and taxa suggest food safety implications. • Endophytic bacteria harbor critical resistance genes like vanX and tet .