Introduction: Early-life establishment of the gut microbiota is essential for host growth, development, and immune function. Owing to developmental limitations of mouse models, the mechanisms by which microbiota-derived metabolites regulate early immune maturation remain incompletely understood. Germ-free pigs, which closely resemble humans in physiology and immune development, provide a valuable model for studying childhood immunity . Objectives: This study aimed to examine the role of gut microbiota in regulating early-life development and immune maturation using germ-free and microbiota-colonized pig models. Methods: Germ-free pigs and conventionally raised controls were established to assess growth and neutrophil function. Singlecell RNA sequencing, single-cell ATAC sequencing, proteomics, post-translational modification proteomics, and metabolomics were integrated to analyze multiple organs and identify key regulatory pathways. Taurine supplementation and molecular approaches were used to evaluate its effects on Jun signaling and neutrophil development. Results: Germ-free pigs showed marked growth retardation and impaired neutrophil development and function. Fecal microbiota transplantation partially restored these defects. Multi-omics analyses revealed reduced taurine levels in germ-free pigs, which were closely associated with immune-related pathways. Further experiments demonstrated that taurine promoted neutrophil maturation through activation of Jun signaling. Taurine supplementation significantly improved neutrophil dysfunction.