The Chinese soft-shelled turtle (Pelodiscus sinensis) is an important freshwater aquaculture turtle due to its taste and nutritional and medicinal value. More ecological culturing modes, such as rice–turtle co-culture, should be developed to meet the ecological benefit demand. We compared growth, physiological parameters, and transcriptome data to detect the physiological responses and regulatory mechanisms of pond-cultured turtles as compared to co-cultured turtles. The co-cultured turtles grew slower than pond-cultured turtles. The gonadosomatic index of co-cultured male turtles was lower than that of pond-cultured male turtles, and both the mesenteric fat index and limb fat index were lower in co-cultured turtles than in pond-cultured turtles (p < 0.05). The blood GLU of the co-cultured turtles was significantly lower than the GLU of the pond-cultured turtles (p < 0.05), while the values of CRE, UA, BUN, AKP, ACP, GOT, and CAT were higher in the co-cultured turtles than in the pond-cultured turtles (p < 0.05). In total, 246 and 598 differentially expressed genes (DEGs) were identified in the brain and gut from turtles cultured in the two different modes, respectively. More DEGs were related to environmental information processing, metabolism, and human diseases. In the brain, the top enriched pathways of DEGs included the longevity regulating pathway, glycerolipid metabolism, cytokine–cytokine receptor interaction, Toll-like receptor signaling pathway, and PI3K-Akt signaling pathway, while in the gut, the top enriched pathways of DEGs included the cell cycle, DNA replication, cellular senescence, and p53 signaling pathway. The turtles acclimated to the different culturing conditions by adjusting their growth, physiological, and biochemical characteristics and related gene expression during a short culture period.

We conducted an 8-week feeding trial to investigate the effect of mixed functional oligosaccharides (chitosan oligosaccharide, fructooligosaccharide, and xylooligosaccharide) extracted from wheat straw on the growth, feeding, physiology, histology, muscle texture, and gut microbiota of Micropterus salmoides. Six diets were formulated by incrementally adding mixed functional oligosaccharides (0.1, 0.5, 1.0, 1.5, and 2.0 mg/kg) to the control diet. 30 individuals with initial body weight of g were randomly allocated to 6 triplicate tanks and fed to apparent satiation twice daily. The fish fed 1.0 mg/kg additives displayed maximum growth, and the feed conversion ratio decreased with the increase in additives from 0 to 1.0 mg/kg ( ) but did not decline further with the addition of more than 1.0 mg/kg ( ). The villus height and width were significantly higher in the supplementation groups than in the control group, while the gut and liver structures presented abnormalities with excessive supplementation above 1.5 mg/kg. There were significant differences in muscle texture indices for M. salmoides over the fed additive gradient, and the hardness, gumminess, and chewiness were highest in the 1.0 mg/kg group. High oligosaccharide levels, such as 2.0 mg/kg, decreased the LZM level, while there were no significant differences in the SOD and MDA levels. Gut microbiome analysis revealed no significant differences in richness and diversity for groups fed the functional oligosaccharide gradient; however, the PCoA results showed that the microbial community composition changed markedly in response to different addition levels, and the 0.5 and 1.0 mg/kg supplementation groups were far apart from the lower and higher supplementation groups. The relative abundance of Proteobacteria was lower in the 0.5 and 1.0 mg/kg addition groups, while that of the phyla Fusobacteria and Firmicutes were higher in these two groups. Functional classification showed that microbes related to carbohydrate metabolism were more abundant in the 0.5 and 1.5 mg/kg groups than in the other groups.