Abstract Background Early-life gut microbiota profoundly influences immune system maturation and disease susceptibility. Perturbations in microbial development have been linked to rising rates of allergic and infectious diseases in children. Probiotic interventions offer a promising strategy to restore microbial-immune homeostasis; however, evidence from rigorously designed, strain-specific randomized trials integrating clinical and microbiome outcomes remains limited. Objective To evaluate the efficacy of Bifidobacterium animalis subsp. lactis XLTG11 in reducing the incidence of eczema and respiratory infections during early childhood, and to explore its associations with gut microbial ecology and immune function. Methods In this randomized, double-blind, placebo-controlled trial, 352 healthy infants and young children (aged 3 years) were randomly allocated to receive XLTG11 (1 × 1010 CFU/day) or placebo for 180 days. Primary outcome was eczema incidence; secondary outcomes included respiratory and gastrointestinal symptoms, growth parameters, gut microbiota composition (16S rRNA gene sequencing), and gut immune biomarkers. Results Children receiving XLTG11 showed significantly lower incidence of eczema (p = 0.017) and erythema (p = 0.028), and a lower incidence of physician-confirmed pneumonia (RR = 0.40, 95% CI 0.17–0.94; p = 0.030) compared with placebo. Probiotic supplementation improved stool consistency (p = 0.018) without affecting growth. 16S rRNA gene sequencing revealed enrichment of Faecalibacterium, Akkermansia, and other short-chain fatty acid–producing taxa, alongside suppression of Helicobacter and Citrobacter. Predictive functional profiling suggested enrichment of pathways related to energy metabolism, vitamin biosynthesis, and antimicrobial peptide (DEFB2, LL-37) production, alongside preservation of secretory IgA. Conclusions Daily B. lactis XLTG11 supplementation safely reduces eczema and respiratory infection risk in early childhood by remodeling the gut microbiome and reinforcing mucosal immunity. These findings support its use as a preventive strategy for allergy and infection via gut-immune modulation. Trial Registration ClinicalTrials.gov (NCT07490587) Ethics Approval Shanghai Sixth People’s Hospital Human Ethics Committee (No. 2023-142)
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