Some Bacillus species present in fermented foods are regarded as probiotics because of their ability to modulate the prevention of some intestinal infections and the modulation of the inflammatory immune response. We isolated bacteriocin-like substances producing Bacillus subtilis and B. lentus from Cheonggukjang, a traditional Korean fermented soybean paste having an inhibitory effect against Salmonella Typhimurium using a well diffusion inhibition assay and a broth co-culturing method. B. subtilis or B. letus was fed to Drosophila melanogaster alone as well as in combination with Salmonella Typhimurium and survival was monitored daily. The survival rates by oral feeding B. subtilis, B. lentus and Salmonella Typhimurium separately resulted in 85, 90 and 75%, respectively. In contrast, survival rates of co-feeding of B. lentus with Salmonella Typhimurium were increased from 75 to 90% during 7 days post-feeding as compared to Salmonella Typhimurium alone. However, B. subtilis in co-feeding with Salmonella Typhimurium significantly reduced D. melanogaster survival rate (85 to 70%). We found that the immune response to B. lentus and Salmonella Typhimurium is characterized synergistic activation of antimicrobial peptide gene expression by Imd pathway. In conclusion, the in vitro and natural-route infection of the D. melanogaster digestive system can result in the use of the probiotic B. lentus for effective treatment of Salmonella Typhimurium infection. We therefore propose the strain B. lentus as a suitable candidate probiotics for use in the prevention and treatment of the intestinal infections caused by Salmonella Typhimurium.