Macrogenomic Analysis Reveals Feeding and Habitat Adaptation Related to the Gut Microbiota of the Non-Obligate Cave Dweller Oreolalax rhodostigmatus (Megophryidae, Anura) among Cave and Culture Environments

The gut microbiota is crucial for host nutrition and adaptation to the environment. The nonobligate cave frog Oreolalax rhodostimatus, which normally inhabit caves year-round. In this study, we compared captive Oreolalax rhodostimatus tadpoles to cave-dwelling Oreolalax rhodostimatus tadpoles to investigate the relationship between gut microbiota and the host’s dietary and environmental adaptations. Macrogenomic analyses showed that Proteobacteria were the most abundant phylum in both cave and captive individuals. However, cave individuals had a significantly higher proportion of Proteobacteria, Firmicutes, and Planctomycetes in their gut microbial community than captive individuals. At the genus level, there was a significant difference in gut microbe composition between cave and captive individuals. Deefgea was found to be more abundant in the gut microbiota of cave individuals, while Bacteroides was more abundant in captive individuals. Combining their gut microbiota with actual action revealed that the Oreolalax rhodostimatus tadpoles are omnivorous. The abundance of metabolic pathways involved proteins and carbohydrates, was significantly higher in captive individuals. This may be due to the fact that cave tadpoles need to expand their food range to ensure energy supply under high survival pressure, compared to captive tadpoles, which showed relatively low feeding pressure. This implies that food resources, gut microbiota, feeding habits, and preferences are all related to habitat adaptation.