Nutrition has a vital role in shaping the intestinal microbiome. The impact of nutrients and the consequences of enteral deprivation on the small intestinal mucosal microbiota, specifically in early life, has not been well described. Our aim was to study the impact of enteral deprivation on the small intestine mucosal microbiome and to search for factors that shape this interaction in early life. Host seem to be the most dominant factor in the structure of the early life mucosal microbial small intestine community. Under conditions of nutrient deprivation, there are specific changes in host proteomics. Further research is needed to better define and understand this host-microbe-nutrition interaction in the small intestine.