Artificial rearing system is commonly used in prolific meat breeds of sheep or in dairy breeds of goats. However, it represents a welfare issue due to increased mortality rates and morbidity. In this study we compared 14 lambs kept with their dams until weaning (mothered=MOT) to their twin counterparts separated 12h after birth from their mothers and reared artificially (ART), to better understand how the rearing mode, and thus the maternal presence, affect GIT microbiome, immunocompetence, health status and performance of lambs until two weeks postweaning. Rumen and fecal microbiota establishment was monitored with qPCR quantification of targeted populations and 16S and 18S amplicon sequencing. Rumen fermentative parameters and serum IgG and sanitary status were measured. Growth was recorded until 2 weeks postweaning. Then, 5 lambs per group were slaughtered, the GIT segments were weighted, and rumen papillae measurements were performed. In rumen and colon tissues, expression of targeted genes encoding for immune function, metabolic activity, and epithelium integrity was measured by RT-qPCR. Early separation with the dam clearly affected digestive microbiota establishment, with a strong delay in colonization by key members of rumen microbiome in ART vs MOT lambs. Fecal concentrations of lactic acid producing bacteria were higher in ART than in MOT in the first weeks of life suggesting differences in fermentation capacities in the hindgut, maybe associated to dysbiosis. A limited immune passive transfer was observed in ART compared to MOT lambs. ART lambs had lower ADG in early phase but finally caught up postweaning. Little or no changes in GIT anatomy, rumen papillae development, or epithelium gene expression were measured at slaughter. The presence of the mother and rearing mode influence GIT microbiota and health associated parameters in offspring in early life and the first month of life is a crucial period in artificial rearing system.