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However, this process the potential factorsaffecting it in the infant are not well known. Moreover, the potential impact of orally administered vaccines, expected to interact with intestinal immune cells eliciting an immune response at mucosal level,upon the establishing microbiome remains unknown.Here we assessed the intestinal microbiome establishmentprocess and evaluated the impact of rotavirus vaccination upon this process. Metagenomic, PCR-DGGE and faecal short chain fatty acids analyses were performed on faecal samples obtained from three infants before and after the administration of each dose of vaccine. We found a high inter-individual variability in the early lifegut microbiota at microbial composition level, but a large similarity between the infants’ microbiomes at functional level. Rotavirus vaccination did not show any major effects upon the infant gut microbiota. 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