R. brelichi
To investigate the potential differences in composition of the microbial community between wild and captive populations, LEfSe was used to analyze the gut microbes of samples from both groups (LDA score of differences (Figure 5). At the phylum level, the relative abundances of Bacteroidota, Spirochaetota, Fibrobacterota, and Desulfobacterota were significantly higher in the captive R. brelichi than in their wild counterparts. In contrast, the relative abundance of Actinobacteriota was significantly higher in wild R. brelichi than in their captive counterparts. At the genus level, the relative abundances of Prevotellaceae_UCG_001, UCG_005 ,Fibrobacter, Sphaerochaeta , Treponema ,Ruminococcus , Bradymonadales (unidentified genus),Faecalibacterium , and Bacteroides were significantly higher in the captive R. brelichi than in their wild counterparts. At the same time, Christensenellaceae_R_7 _group,Clostridia_UCG_014 , dgA_11_gut_group ,Pseudomonas , Acinetobacter , RF39 , andAkkermansia were more abundant in wild R. brelichi .
3.4 Predicted functional differences of the gut microbiota between wild and captive R. brelichi
We performed analysis of KEGG metabolic pathways in both captive and wild R. brelichi . In KEGG Level l categories, the gut microbial genes of captive and wild R. brelichi were associated with six types of metabolic pathways (Figure 6a), three of which exhibited significant differences. Specifically, the enrichment of environmental information processing genes was significantly higher in wild R. brelichi than in captive R. brelichi , while the opposite pattern was observed for genes involved in genetic information processing and organismal systems (Figure 6b). In KEGG Level 2 categories, the gut microbial genes of captive and wild R. brelichi were associated with 32 types of metabolic pathways (Figure 6a), among which 15 differed significantly (p < 0.05). Specifically, the captive group showed significant enrichment of pathways such as cell growth and death, replication and repair, translation, amino acid metabolism, biosynthesis of other secondary metabolites, carbohydrate metabolism, glycan biosynthesis and metabolism, infectious diseases, immune system, digestive system, and endocrine system. Meanwhile, the wild group showed significant enrichment of pathways such as membrane transport, signal transduction, xenobiotics biodegradation and metabolism, and lipid metabolism (Figure 6c).