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The symbiotic microbiota inhabiting the skin and gut of amphibians exerts roles in maintaining host health, especially during the critical stage of complete metamorphosis where failure to remodel the microbiota can result in various diseases. However, the composition and alterations in the amphibian microbiota in diverse diseased populations, as well as the exact mechanisms underlying disruptions in skin and gut microbial communities leading to diseases, are not yet well established. Herein, skin and gut microbiota were sampled from healthy Chinese spiny frogs (CTL group) as well as individuals with ascites disease (AD group), cataract disease (CD group), and rotten-skin disease (RD group) for Illumina high-throughput sequencing analysis to comprehensively explore potential associations between microbiota composition and the health status of the host. Venn diagrams and UpSet analysis revealed that the CTL group exhibited the highest number of unique amplicon sequence variants (ASVs) in their skin, while the CD group displayed the lowest abundance of ASVs in their gut. Compared to the CTL group, the alpha-diversity of skin microbiota was dramatically depressed in diseased groups, and notable variations in the beta-diversity of both skin and gut microbiota were observed. Further compositional analysis identified Firmicutes, Proteobacteria, and Bacteroidota as the dominant bacterial phyla in both skin and gut microbiota, although their relative abundances varied widely among groups. The linear discriminant analysis effect size (LEfSe) analysis identified various bacteria species with substantial differences between skin and gut microbiota groups including beneficial populations as well as opportunistic ones. Functional predictions indicated significant differences between CTL and diseased groups mainly enriched in metabolism-relevant pathways. Furthermore, in vitro culture experiments confirmed the presence of a total of 19 strains of bacteria from the skin microbiota of RD group, including opportunistic bacteria population Acinetobacter closely associated with spiny frog rotten-skin disease. Taken together, this work provides insights into the composition dynamics of skin and gut microbiota under different health conditions in spiny frogs, highlighting potential applications for symbiotic microbiota modification in promoting healthy amphibian culture practices as well as preventing diseases. • Diseases significantly impacted alpha-diversity and beta-diversity of skin and gut microbiota in Chinese spiny frog. • Firmicutes, Proteobacteria, and Bacteroidota might be intrinsic microbiota colonizing skin and gut of Chinese spiny frog. • Several sensitive indicator taxa were identified for host health assessment and disease prediction. • Diseases triggered biological dysfunctions in microbiota of Chinese spiny frog, especially pathways related to metabolism. • Skin-cultivable bacteria were identified from frogs with rotten-skin disease, dominated by opportunistic pathogens. [ABSTRACT FROM AUTHOR]