Bifidobacterium longum subsp. infantis and Bifidobacterium adolescentis play important roles in the guts of infants and adolescents, respectively. In this study, using a neonatal rat model, we compared the protective effects of these 2 bifidobacterial species against Salmonella infection. The results demonstrated that B. longum subsp. infantis was more effective than B. adolescentis in alleviating the severity of infection in newborn rats exposed to Salmonella enterica serovar Typhimurium strain SL1344. B. longum subsp. infantis attenuated intestinal inflammation and mucosal damage induced by Salmonella infection, as well as protecting intestinal nerves and intestinal barrier function through TLR4/MyD88 signalling. B. longum subsp. infantis also displayed the potential to modulate gut metabolites by promoting the biosynthesis of unsaturated fatty acids (arachidonic acid, eicosapentaenoic acid and α-linolenic acid) and purine metabolism (guanine, adenine, inosine and adenosine), thereby regulating metabolic disturbances. Additionally, the benefits of B. longum subsp. infantis were also observed in the liver, spleen and brain, improving nerve reflexes and suppressing hepatosplenomegaly. Overall, these findings provide novel insights into the prevention and treatment of gut-related diseases in newborns, highlighting the potentially significant role of B. longum subsp. infantis in clinical applications.