Purpose The development of probiotics has seen tremendous growth over the years, with health benefits ranging from gut health to respiratory. We thus aimed to investigate the effects of probiotic Bifidobacterium lactis Probio-M8 (2 × 10 10 log CFU/day) against acute respiratory tract infections (RTI), use of antibiotics, hospitalization period and elucidate the possible mechanisms of action in hospitalized young children. Method A prospective, randomized, double-blind and placebo-controlled study was performed in RTI-hospitalized children. Patients were randomized to either the probiotic (n = 60, mean age 13.81 ± 0.90 months) or placebo (n = 60, mean age 12.11 ± 0.73 months) which were administered upon admission, continued during hospitalization and 4-week post-discharged. RTI and gut health parameters were assessed at these time points using validated questionnaires while concentrations of inflammatory cytokines were assessed via oral swabs. Results Probio-M8 reduced the duration of nasal, pharyngeal and general flu-like symptoms compared to the placebo during the hospitalization period and 4-week post-discharged (P < 0.05) as compared to the placebo, with a more prevalent effect against lower respiratory tract infections (LRTI). Probio-M8 reduced prescription of antibiotic (P = 0.037), prevented new prescription of antibiotic in non-prescribed patients (P = 0.024) and reduced hospitalization period in antibiotic-prescribed patients (P = 0.004) as compared to the placebo. Oral cytokine levels of TNF-α decreased in the Probio-M8 group (P = 0.001) accompanied by increased in IL-10 (P = 0.018) over 4-week post-discharged, while the placebo group did not exhibit such an effect. Increased IL-10 in the Probio-M8 group was correlated with decreased body ache (r = − 0.296, P = 0.001), headache (r = − 0.295, P = 0.001) and pain during swallow (r = − 0.235, P = 0.010). Conclusion Data from our present study show that B. lactis Probio-M8 could be a potential natural and non-drug strategy for the management of RTI in young children in a safe manner. Clinical trial registration Clinical studies (Approval No. USM/JEPeM/19030177) were registered at ClinicalTrials.gov (Identifier No. NCT04122495) on September 30, 2019.

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