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As global demand for milk and meat increases, young ruminants need rapid gut development and sufficient mucosal immunity immediately after birth. However, their growing intestines face oxidative and microbial challenges that can harm long-term performance. This review systematically summarizes recent advances in how host genetics, early nutrition, and emerging microbiota interact to influence intestinal development and mucosal immunity under standard rearing conditions. We explore how the host regulates the gut microbiota, the microbiota's role in maintaining gut integrity, barrier function, development, intestinal cell health, mucosal immunity, and how diet modulates gut microbiota composition in young ruminants. Microbial signals promote increased villus length and better epithelial functions. Conversely, dysbiosis delays gut closure, weakens barrier integrity, and skews immunity toward proinflammatory responses. Feeding strategies such as colostrum timing, milk replacers, and the addition of starter fiber and probiotics can alter microbial communities within days. Nonetheless, challenges remain in standardizing neonatal feeding practices, identifying microbe metabolite indicators of gut health, and integrating precision feeding technologies. By mapping the three-way interaction among host, microbiota, and diet, this review offers a blueprint for neonatal ruminant feeding that enhances both animal welfare and the productivity of future ruminant systems. This review also provides a novel mechanistic integration of host genetics, gut microbiota succession, and dietary interventions in young ruminants, filling the gap of fragmented multi-omics analyses in existing literature and offering targeted insights for optimizing gastrointestinal development and production efficiency.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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