The establishment of the infant intestinal microbiome is not affected by rotavirus vaccination

Abstract

The microbial colonization of the intestine during the first months of 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, the potential factors affecting this process in the infant are not well known. Moreover, the potential impact of orally administered vaccines upon the establishing microbiome remains unknown. Here we assessed the intestinal microbiome establishment process 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 life gut 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 rotavirus vaccination appears to be inconsequential for this process.

Figure 1. PCR-DGGE faecal microbiota profiles obtained before and after (b or a) each rotavirus vaccination dose (D1, D2 and D3) from each infant.

Numbers indicate the results of the species identification of the corresponding DGGE band.

Figure 2. PCoA analysis of the microbiota composition at genus level obtained from faecal samples before and after (b or a) each rotavirus vaccination dose (D1, D2 and D3) from each infant.

PCoA was performed with Spearman correlation distance.

Figure 3. Main faecal microbial groups at genus level (A) and gene functional annotations at KEGG level 2 (B) determined from the metagenomic analyses of the samples obtained at different time points from each infant.

Figure 4. Spearman's distances (mean and sd) obtained by comparing data at functional KEGG level B, functional KEGG level C and microbial composition (genus level) from all the samples from the different infants at each time point.