Prebiotics are compound that selectively enhance the growth of beneficial gut bacteria. They have been recommended and used in infant formula and weaning cereals resulting in gut microbiota resembling that of breastfed infants in formula fed infants in developed countries. A healthy gut microbiota was shown to be associated with enhanced growth patterns and decreased morbidity in children in developed countries. Evidence of such outcome is lacking in developing countries, yet such results would be particularly valuable for children from these settings, living in rather poor sanitary conditions in an environment characterized with high infectious disease load, conditions that mostly explain the high prevalence of chronic malnutrition. This study aims to assess the effect of a 6 months' supplementation with a lipid based nutrient supplement fortified with fructo-oligosaccharides and inulin on microbiota diversity and functionality in rural Burkinabe infants, and to explore its subsequent effects on linear growth velocity and morbidity.