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

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.