Seasonal dynamics of gut microbiota in Chinese soft-shelled turtles (Pelodiscus sinensis): Implications for sustainable aquaculture practices

Abstract

The gut microbiota significantly influences host health, yet its seasonal dynamics in reptiles—especially in farmed species like Chinese soft-shelled turtle (Pelodiscus sinensis)—remain largely unexplored. Considering the unique physiology of reptiles and their distinct seasonal behaviors, understanding these dynamics is crucial for optimizing management strategies. This study investigated seasonal changes in the gut microbiota of Chinese soft-shelled turtles and the underlying community assembly mechanisms. Large intestine samples were collected and analyzed using 16S rRNA gene sequencing, with seven samples obtained each season. Results indicated that summer exhibited significantly higher richness than autumn and winter, as confirmed by the Shannon and Simpson indices, while evenness was significantly greater in summer compared to autumn with a near-significant trend versus winter (P = 0.053). Beta diversity analysis showed significant seasonal clustering, indicating seasonality's impact on the gut microbiota structure. Dominant phyla included Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteriota. The relative abundance of Bacteroidota increased during autumn and winter, while Firmicutes decreased, suggesting an energy source shifts during hibernation. Functional predictions indicated seasonal differences in glycan biosynthesis and metabolism pathways. Community assembly analysis indicated increased stochastic processes in autumn and winter, while deterministic processes dominated in summer. This shift towards stochastic processes during colder seasons likely results from greater environmental variability, such as temperature fluctuations and reduced food availability. Fourteen operational taxonomic units were shared across all seasons, displaying cooperative interactions. The presence of potentially pathogenic genera like Edwardsiella and Aeromonas in winter suggested a possible link to post-hibernation mortality. These findings provide valuable insights into how Chinese soft-shelled turtles adapt to seasonal changes through gut microbiota shifts, offering improved knowledge for aquaculture management.