The acquisition and development of the infant microbiome plays a key role in healthy host-microbiome symbiosis. The neonatal and infancy periods are most important stages in the establishment of the intestinal microbial community. There are many maternal factors plays a major role in acquiring the balanced gut microbiota during birth. Moreover, continuous acquisition of nascent microbiome is a relatively dynamic process influenced by breastfeeding practices, weaning to solid food antibiotics and other practices. Therefore, development of the gut microbiota in infancy occurs during a ‘critical window,’ and a disturbance in this process may cause many health problems. The current interactions and associations of the early-life exposures on the development and colonization of the gut microbiota in infants and disease conditions requires further researches to determine the causes.