Secondary adaptation of amphibians to marine environments is exceptionally rare. The crab-eating frog, Fejervarya cancrivora, is the only known amphibian capable of completing its life cycle in intertidal zones, where it faces dual challenges: high salinity stress and a diet rich in chitinous crab exoskeletons. While osmoregulatory adaptations have been well documented, the synergistic roles of the host's digestive system and its gut microbiota in this dietary specialization remain unclear. Here, we integrated histological analysis, comparative transcriptomics, chitinase activity assays, and gut metagenomics to compare F. cancrivora with its freshwater congener, F. multistriata. We found that F. cancrivora has evolved a thicker gastric muscularis and longer gastric villi, consistent with enhanced processing of hard prey. Comparative transcriptomic analysis revealed an expanded repertoire of putative chitinase encoding transcripts (15 vs. 8 non-redundant transcripts), and both gastric and intestinal tissues exhibit significantly higher and more pH-tolerant chitinase activity. In contrast, the gut microbiota of F. cancrivora is not enriched for microbial chitin degradation genes, but instead is functionally specialized for lipid metabolism and DNA repair pathways. A controlled feeding experiment confirmed that the microbial enrichment in lipid metabolism is diet-driven, while the DNA repair pathways is largely independent of diet and likely reflects microbiome-intrinsic adaptation to chronic saline stress. Together, these findings suggest a partially partitioned host-microbiome strategy in which host manages chitin breakdown, while the microbiota optimizes energy harvest and intrinsic stress tolerance. Our findings provide a new paradigm for amphibian marine adaptation, and highlights host-microbiome functional differentiation during niche expansion.
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