The gut microbiota plays a crucial role in promoting food digestion in animals. However, the impact of cross-species microbiota transplantation from donors with different dietary habits on the host food digestion capacity remains unclear. Objective To investigate the role of cross-species microbiota transplantation in regulating the digestive system adaptability, metabolic functions, reproduction, stress responses, and gut microbiota structure of the host. Methods We utilized New Zealand white rabbits (Oryctolagus cuniculus), a herbivorous species, and C57BL/6J mice, an omnivorous species, as donors and recipients of gut microbiota, respectively. The mice were allocated into three groups: a control group on a normal diet (Con), a group on a high-fiber diet (TS), and a group on a high-fiber diet supplemented with rabbit fecal microbiota transplantation (OC). This study was designed to evaluate various physiological and biochemical parameters, including body weight, food intake, absolute and relative organ weights (both wet weight and organ-to-body weight ratio), morphometric indices (length and diameter) of the small intestine, sperm concentration, and serum corticosterone level, in mice. Additionally, we performed 16S rRNA gene sequencing targeting the V3-V4 hypervariable region to characterize the composition of fecal microbiota. Results A high-fiber diet significantly increased the food intake, small intestine length, and serum corticosterone level, while significantly reducing the body weight, liver and spleen wet weights, liver/body weight ratio, spleen/body weight ratio, and sperm concentration in mice. Moreover, it increased the alpha diversity of the gut microbiota, decreased the Bacillota-to-Bacteroidota ratio, and reduced the relative abundance of probiotics (such as Ligilactobacillus). Transplantation of the gut microbiota from rabbits increased the wet weight of the epididymis and the epididymis/body weight ratio, while significantly reducing the liver/body weight ratio and the serum corticosterone level in recipient mice. Furthermore, a high-fiber diet significantly increased the relative abundance of the fiber-degrading bacterial family (Oscillospiraceae) and the gut health-associated bacterial genus (Colidextribacter). After the transplantation of rabbit gut microbiota into mice, the relative abundance of Oscillospiraceae and Colidextribacter in mice increased significantly. Conclusion The high-fiber diet has adverse effects on omnivores. Although the microbiota transplantation from herbivores does not significantly improve the host ability to digest fiber, it changes the gut microbiota structure of omnivores, playing a positive role in improving their digestion, reproduction, metabolism, and stress responses. Future research needs to further determine the optimal levels of dietary fiber for omnivores and the dosage of microbiota transplantation from herbivores, as well as their synergistic effects and underlying mechanisms in improving animal health. This study provides a reference for exploring the role of gut microbiota in animal adaptation to dietary changes in natural environments and lays a foundation for future research on improving the utilization of high-fiber foods by omnivorous domestic animals.