Abrupt environmental changes upon weaning provide critical challenges to young animals that are dietary and other external stressors causing mucosal immune reaction in the small intestine. Intestinal environment and health are largely influenced by the mucosal immune reaction resulting in villus destruction and repairing, alteration to nutrient utilization, and finally growth efficiency. This special issue covers the original research and in depth review in relation to dietary and external challenges affecting intestinal microbiota and mucosal immune response affecting nutrition and growth efficiency of young animals. Please refer to oursubmission guidelinesfor information on preparing your manuscript and submit your manuscript via ouronline submission system. To ensure that you submit to the correct thematic series, please select the appropriate section in the drop-down menu upon submission. Each manuscript will be peer-reviewed using the journal's usualpeer reviewprocess. Journal of Animal Science and Biotechnology is a leading open access journal publishing innovative research across agriculture, dairy and animal science.