The microbial colonization of the intestine during the first monthsof life constitutes the most important process for the microbiota-induced host-homeostasis.Alterations in this process may entail a high-risk for disease in later life. However, this process the potential factorsaffecting it in the

The microbial colonization of the intestine during the first monthsof life constitutes the most important process for the microbiota-induced host-homeostasis.Alterations in this process may entail a high-risk for disease in later life. 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. Thus, the individual microbiome establishment and development process seems to occur in a defined manner during the first stages of life and it is not affected by oral rotavirus vaccination.