Environmental enrichment is associated with changes in the gut microbiome and resistome of captive pythons

Environmental enrichment is widely used to improve the welfare of captive animals, yet its effects on reptilian gut microbiota remain poorly understood. Here, we used shotgun metagenomic sequencing to investigate the gut microbiome and resistome of two captive python species: Burmese python ( Python bivittatus) and reticulated python ( Malayopython reticulatus) , before and after environmental enrichment. We found that environmental enrichment was associated with increased α-diversity in Burmese pythons, as indicated by significantly higher ACE and observed species indices, while NMDS ordination revealed differences in the observed patterns of community composition between the two species. Pseudomonadota and Bacteroidota were dominant phyla in the gut microbiota of both python species, but their relative abundances responded differently to enrichment between hosts. Functional analyses suggested an enhanced metabolic potential in Burmese pythons, particularly in carbohydrate metabolism and environmental information processing, accompanied by increased abundance of carbohydrate-active enzymes. In addition, enrichment may influence the gut resistome, with Pseudomonadota contributing the majority of antibiotic resistance genes. Overall, our results demonstrate that environmental enrichment measures, such as dietary changes and improvements in water and air quality, are associated with changes in the gut microbiome and resistome of captive pythons in a host-dependent manner, highlighting the combined roles of diet and environmental conditions in the observed changes in the gut microbiota. These findings provide exploratory insights into the functional responses and host–microbiome evolution of reptile gut microbiota to captivity and have important implications for the management and welfare of captive animals.