Newborn animals are immediately exposed to a diversity of microorganisms: vaginal and skin microbiota of mothers and other environmental microbes that colonize the gastrointestinal lumen and gradually establish gut microbiota during development. The premature microbiota in infancy develops into more stable microbial communities in childhood. Pertubations of gut microbiota early in life have been associated with susceptibilities to multiple immune and metabolic diseases, including asthma, atopic dermatitis, inflammatory bowel disease, and obesity, occurring later in life. Furthermore, administration of antibiotics during pregnancy increases susceptibilities to immunological and metabolic disorders of offspring. Thus, the prenatal and infant periods are regarded as critical time-windows for long-term health status. In this review, we describe our recent understanding of how the disturbance of early-stage microbiota cause pathological imprinting in immune and metabolic systems. We also discuss how microbial products shape host immune and metabolic configurations.