Season dominates and housing system conditionally modulates the gut microbiota of red pandas

The gut microbiota critically influences host nutrition and immunity, yet the combined effects of housing systems and season on endangered bamboo-feeding mammals remain unclear. We analyzed the gut microbial diversity, community structure, and potential metabolic functions of captive and free-range red pandas ( Ailurus styani ) across winter–spring and summer–autumn seasons. Season emerged as the primary driver of microbial richness and community structure, with higher richness in winter–spring and greater seasonal amplitude in free-range than captive red pandas. Housing effects were significant only in summer–autumn, when free-range individuals showed higher Shannon/Simpson diversity and distinct community separation from captives. Dominant phyla were Firmicutes (65.17%) and Proteobacteria (26.76%). Differential enrichment included Streptococcus in captive summer–autumn, Lactococcus/Leuconostoc in free-range summer–autumn, Escherichia-Shigella / Staphylococcus in captive winter–spring, and genus 1174-901-12 (an uncultured genus within the family Ruminococcaceae) in free-range winter–spring. Based on KEGG prediction, free-range individuals exhibited stronger seasonal functional potential differences; they were enriched in 17 pathways, including amino acid metabolism and energy metabolism, in winter–spring, and shifted toward carbohydrate metabolism and membrane transport in summer–autumn, with additional enrichment in xenobiotics biodegradation and metabolism pathways. In contrast, the functional potential shift in captive individuals was relatively limited. In summary, seasonal variation dominated the structural remodeling of the gut microbiota in red pandas, while housing system acted as a conditional regulatory factor whose effect was significantly amplified in summer–autumn. This study suggests that the free-range pattern may help maintain gut microbiota diversity, structural stability, and metabolic functional potential. This study provides a microecological basis for gut health management in endangered bamboo-eating mammals.