Gut microflora is acknowledged as a major contributor to Health whatever the physiological stage. In the neonatal period, microbial colonization of the infant gut is essential for the development of the intestinal and immune systems. The profile of intestinal microbiota is influenced by genetics and environment, including the route of delivery and early dietary intake. The microbiota of full-term, vaginally delivered, breast-fed infant is considered as ideally healthy. Human milk consumption shapes the infant microbiota thanks to its unique mix of antimicrobial proteins, abundant sIgA, but also milk fat components such as polar lipids and a broad range of fatty acids that may influence the ecology of the neonatal microbiota. Structure, composition and physiological properties of Human milk are better mimicked in infant formulas that include milk lipids and milk fat membrane extracts although very few infant formulae use milk lipids more expensive than vegetable lipids. In this context, two formulas based on i) vegetable fat (STD) or ii) a blend of vegetable fat and milk lipids stabilized by milk fat membrane extracts (EXP) were distributed with an automatic milk feeder to piglets from birth until 28 days. At this stage, feces were collected and analyzed in terms of microbial diversity by metasequencing (16S rRNA extraction and sequencing, GS-FLEX 454 Roche). The EXP formula modified positively the microbiota with an increase in proteobacteria and a decrease in firmicutes. This shift is also observed in breast-fed compared to formula-fed 6 mths-old neonates.In conclusion, the milk fat addition in infant formulas modulated the intestinal microbiota. The persistence of these modifications and their impact on adult metabolism will be further investigated to elucidate the links between early milk fat intake, intestinal maturation and microbial colonization of the infant gut.