Digestive Tract Structure and Seasonal Dynamics of Gut Microbiota in Hypomesus nipponensis from Bosten Lake

Digestive tract structure is a key indicator of fish health and environmental adaptation, while seasonal dynamics of the gut microbiota reflect host responses to environmental changes. In this study, the digestive tract microstructure of Hypomesus nipponensis from Bosten Lake was characterized using H&E staining and scanning electron microscopy, followed by 16S rDNA gene V3-V4 region sequencing and analysis of the gut microbiota in spring, summer, and autumn. The results showed that the esophageal mucosa of H. nipponensis is a stratified columnar epithelium, with abundant gastric glands, and the circular muscle layer of the stomach caeca is significantly thickened (244.84 ± 49.01 μm). The pyloric caeca resemble the gut in structure; both are covered with dense microvilli on the luminal surface. Collectively, these features constitute the structural basis for its carnivorous diet. Microbiota analysis revealed that the diversity of gut microbiota fluctuated significantly with season: the Chao, Ace, and Sob indices in spring (144.63 ± 30.27) were significantly higher than in summer (82.13 ± 21.45) and autumn (83.25 ± 15.30) (p < 0.001), with no significant difference between summer and autumn (p > 0.05). The dominant marker genera of H. nipponensis in spring, summer, and autumn were Bacillus (31.60%), Clostridium (32.20%), and Sarcina (29.32%), respectively. This study describes the adaptive characteristics of the digestive tract structure and feeding habits of H. nipponensis and reveals the seasonal changes in its gut microbiota. Importantly, since the digestive tract structure data were collected only in summer, the direct relationship between the structure and seasonal microbial dynamics cannot be determined, and multi-season histological sampling is needed for further investigation. Nevertheless, these findings provide preliminary morphological and microbiological references for the ecological adaptation of this species in Bosten Lake and offer a scientific basis for water resource management in this area.