The human microbiota plays a key role in early development of neonate and significantly influences the child’s health. Mother milk is sole source of nutrition for infants and lately it has proven to be a main and continuous source of microbial inoculum for gut colonization of infants. These early gut microbial inhabitants stimulate the immune systems and plays vital role against the pathogenic invasion. Thus, delineate the factors affecting the milk microbiota of lactating mother would provide an important insight on the infants gut colonization. In India, to the support the nutritional requirement, lactating mothers, are supplemented with various traditional food preparation rich in complex carbohydrates, fats and protein. We investigated the impact of complex oligosaccharides present in the supplements on milk microbiota of lactating mothers and its implication in neonatal health.