A positive correlation between gut microbiome compositional variations and dietary shifts across different stages encompassing the entire active period in Shinisaurus crocodilurus

The composition of the gut microbiome can rapidly respond to dietary changes. The Chinese crocodile lizard (Shinisaurus crocodilurus) is an endangered and evolutionarily unique species that urgently requires research. However, the impact of dietary changes on the adaptation of intestinal microorganisms remains unexplored. In this study, we examined the structure and temporal dynamics of gut bacterial communities, characterized dietary composition and shifts, and evaluated the association between dietary variation and gut microbiome alterations across three stages (Stage I, post-hibernation breeding stage; Stage II, stable active stage; Stage III, pre-hibernation stage). Our results revealed that four phyla dominated the gut microbiota (Firmicutes, Proteobacteria, Bacteroidota, and Fusobacteriota). While alpha diversity remained stable, beta diversity significantly differed across stages. Stage I exhibited the highest number of taxa with increased relative abundance and the greatest number of differentially abundant microbial taxa, and Moraxellaceae was identified as both a differentially abundant taxon and a key microbial biomarker in this stage. Furthermore, Insecta, Malacostraca, and Arachnida constituted the primary dietary components at the class level. Although prey taxonomic groups were largely consistent, significant differences in diet composition were observed across stages. Notably, a pronounced predation on Clitellata occurred exclusively in Stage I, contrasting with Stages II and III, where Insecta dominated the diet, indicating a clear dietary shift. Trophic niche width (TNW) at the population level was relatively broad overall, yet narrowest at both population and individual levels during Stage I, coinciding with the highest degree of individual specialization (IS). Gut microbiome variations were strongly correlated with dietary differences, with specific prey orders exerting marked influences on microbial community structure. These findings provide critical insights into the dynamic interplay between diet and gut microbiota in response to different stages, and these are vital for guiding conservation initiatives in the Chinese crocodile lizard.