Probiotic bacteria exhibiting antagonistic activities against pathogenic bacteria are widely considered as potential options for the prevention and treatment of various infectious diseases and represent potential substitutes of antibiotics. Here we show that theL. plantarumAG10 strain represses the growth ofStaphylococcus aureusandEscherichia coliin vitro and diminishes their negative effects in vivo in aDrosophila melanogastermodel of survival on embryonic (larvae) and pupa stages. In an agar drop diffusion test,L. plantarumAG10 exhibited antagonistic properties againstEscherichia coli,Staphylococcus aureus,Serratia marcescensandPseudomonas aeruginosa, and repressed the growth ofE. coliandS. aureusduring milk fermentation. In aDrosophila melanogastermodel,L. plantarumAG10 alone did not provide any significant effect, either during the embryonic stage or during further development of the flies. Despite this, it was able to restore the viability of groups infected with eitherE. coliandS. aureus, almost to the level of non-treated control at all stages of development (larvae, pupa and adult). Moreover, in the presence ofL. plantarumAG10, pathogens-induced mutation rates and recombination events reduced 1.5–2-fold. The genome ofL. plantarumAG10 was sequenced and deposited at NCBI under the accession number PRJNA953814 and consists of annotated genome and raw sequence data. It consists of 109 contigs and is 3,479,919 bp in length with a GC content of 44.5%. The analysis of the genome has revealed considerably few putative virulence factors and three genes responsible for the biosynthesis of putative antimicrobial peptides, with one of them exhibiting a high probability of antimicrobial properties. Taken together, these data allow the suggestion that theL. plantarumAG10 strain is promising for use in both dairy production and probiotics as a preservative from foodborne infections.