Climate warming induces age-specific gut microbiota alterations and functional metagenomic changes in captive crocodile lizards (Shinisaurus crocodilurus)

Host-microbiota interactions may influence species’ adaptability to global climate warming, yet data are scarce for endangered, narrow climatic niches. We integrated 16S rRNA sequencing, metagenomics, and morphometric to explore age-specific gut microbiota responses of captive crocodile lizards (Shinisaurus crocodilurus) to simulated warming (+1.3–2.4°C) over 2, 4 and 6 months. Six-month warming revealed age-structured divergence: juveniles showed significant losses in Firmicutes and Actinobacteriota, with Yokenella correlating with reduced body mass. In adults, diversity declined only at 6 months, linked to significantly decreased Acidobacteriota and Actinobacteriota. Metagenomic profiling in juveniles revealed warming-driven functional shifts: ABC transporters and Two-component system were significantly diminished, while Carbon metabolism pathways were significantly enriched. Warming was also associated with shifts in opportunistic taxa, with several putative pathogens increasing in relative abundance. Overall, prolonged modest warming reduced gut microbiota diversity and altered functional potential, with juveniles disproportionately affected. Our findings establish gut microbiota as biomarkers of climate resilience, emphasize the need for age-specific conservation strategies, and provide theoretical basis and reference for scientific conservation of endangered species with narrow climatic niches, which could help predict and mitigate the impacts of climate warming on endangered species.