The infant microbiota have a great impact on development of childhood diseases. There is a remarkably increased risk of complications. Disruption of the transmission of maternal microbiota to neonates results in increased possibilities of certain childhood diseases. Breastfeeding makes babies well-nourished and prevents them from being obese and suffer from other chronic illnesses in their later life. Undernourished infants are prone to infections caused by pathogenic microorganisms and have reduced levels of beneficial bacteria and reduced microbiome diversity in their gastrointestinal tract. Neonatal antibiotics exposure also causes several unwanted outcomes including NEC, invasive fungal infection, growth impairment and obesity.