The micorbial pattern of mice and infants is described in comparison of luminal and mucosa associated microbiome.

Environmental factors including nutritional habits or birth mode are known key determinants for intestinal microbial composition. Investigations of the intestinal microbiome in different species in a multiplicity of studies during the last decades have revealed differential microbial pattern and quantity along the gastrointestinal tract. Characterization of the microbial pattern in various aspects is a prerequisite for nutritional interventions: In this 16S rRNA amplicon based approach we present a characterization of the mucosa-associated microbiome in comparison to the luminal community of five infants at the time of closure of enterostomies and perform a systematic characterization of the corresponding luminal and mucosal microbiome from jejunal, ileal and colonic regions as well as collected feces in mice. The most dominant taxa in infants´ derived samples altered due to individual differences and in the mucosa Enterococcus, Clostridium sensu stricto 1, Veillonella, Streptococcus and Staphylococcus were the most abundant. Three less abundant taxa differed significantly between mucosa and lumen. In murine samples, relative abundances differed significantly mainly between the intestinal regions. Significant differences between mouse mucosa and lumen derived samples could be found in the observed species with a trend to lower estimated diversity in mucosa derived samples as well as in the relative abundance of individual taxa. In this study we have examined the difference between mucosal and luminal bacterial colonization of the gastrointestinal tract in a small sample cohort of infants. Individual differences were characterized and reached statistically significance in three taxa (Elizabethkingia, Cupriavidus, Ralstonia). The corresponding study on the different murine intestinal regions along the GI tract showed differences all over the intestinal region.