Metagenomic analysis reveals hidden links between gut microbes and habitat adaptation among cave and surface dwelling Sinocyclocheilus species

Intestinal microbes are closely related to vital functions for the host such as food digestion and nutrient absorption, which plays an important role in enhancing host adaptability. As a natural “laboratory,” a cave habitat provides an outstanding model for understanding the significance of gut microbes and feeding habits in a host’s habitat adaptability. However, research on the relationship between gut microbes, feeding habits, and the adaptability of troglobites is insufficient. In this study, we compared the characteristics of the intestinal microbes of Sinocyclocheilus cavefishes and surface fishes and further established the relationship between intestinal and habitat microbes. Furthermore, we also conducted eDNA (metabarcoding) analysis on environmental samples to clarify the composition of potential food resources in habitats of the Sinocyclocheilus cave and surface fishes. The results show that the structure of Sinocyclocheilus gut microbes is more related to the ecological type (habitat type) than phylogenetic relationships. However, the horizontal transfer of habitat microbes is one source of fish gut microbes, but the host shows a strong selection for  inherent microbes as predominant microorganisms. The difference in composition and structure of gut microbes, especially predominant microbes, can enhance the adaptability of the two Sinocyclocheilus fish types from the perspectives of food intake, nutrient utilization, and harmful substance metabolism. Such links eventually form a closed loop of habitat adaptability through food resources, predation pattern, intestinal flora, digestive and absorptive capacity, and feeding habits and preferences. The obtained results facilitate our understanding of the significance of fish gut microbes to habitat adaptation and provide a new perspective for studying the adaptive mechanisms of cave fishes.