Objectives:The aim of the study was to assess the effect of nutritional supplementation with lipid-based nutrient supplements (LNS) and corn-soy blend flour on Bifidobacterium and Staphylococcus aureus gut microbiota composition in Malawian infants. In addition, the microbiota changes over time were characterized in the study infants. Methods:Healthy 6-month-old Malawian infants were randomly assigned to 1 of 4 intervention schemes for a 6-month period. Infants in the control group were not provided with any supplementary food. Infants in other 3 groups received either micronutrient-fortified corn-soy blend, micronutrient-fortified LNS with milk protein base, or micronutrient-fortified LNS with soy protein base between 6 and 12 months of age. Fecal bifidobacteria and S aureus gut microbiota at 6 and 12 months of age were analyzed by quantitative real-time polymerase chain reaction method. Results:There was no difference in change in bacterial prevalence or counts between the intervention groups during the 6-month study period. When looking at the total study population, higher counts of total bacteria (P=0.028), Bifidobacterium genus (P=0.027), B catenulatum (P=0.031), and lower counts of B infantis (P<0.001), B lactis (P<0.001), B longum (P<0.001), and S aureus (P<0.001) were detected in the children's stools at 12 months rather than at 6 months of age. Conclusions:The dietary supplementation did not have an effect on the Bifidobacterium and S aureus microbiota composition of the study infants. The fecal bifidobacterial diversity of the infants, however, changed toward a more adult-like microbiota profile within the observed time.