Abstract
BACKGROUND: Weaning represents a critical period during which mammals adapt to solid food and develop their immune systems. The intestine, as the primary digestive and immune organ, is central to successful weaning. Bats are the only flying mammals and undergo ontogenetic shifts in flight and diet in response to substantial energy and immune demands. However, the transcriptomic and metabolomic changes in bat intestines during the weaning transition remain unexplored. RESULTS: In this study, 24 small intestinal tissue samples were collected from Vespertilio sinensis across four developmental stages, ranging from new-born to weaned. The analysis identified 7,545 significantly differentially expressed genes (DEGs) and 1,006 metabolites, which were enriched in metabolomic pathways related to nutrient digestion, signal transduction, and immunity. Several highly expressed genes were identified in carbohydrate digestion (TREH, MGAM, and SI), lipid metabolism (CD36, ABCG5, ABCG8), protein digestion (CPA1 and CPB1), taste transduction (SCNN1B and SCNN1G), and immune response (FUT2 and SUCNR1). Additionally, major metabolites, including cholic acid, acetylcholine, serotonin, and uric acid, were implicated in dietary shifts in young V. sinensis during weaning. CONCLUSIONS: This is the first study to investigate transcriptomic and metabolomic changes in the small intestine of insectivorous bats during weaning. These findings enhance our understanding of the small intestine’s role in ontogenetic dietary shifts and provide novel insights into the molecular mechanisms underlying weaning in wild mammals. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-025-11784-7.