QIIME 2整合分析发酵饲料对不同动物肠道微生物群落的影响

QIIME 2-based integrative analysis of the effect of fermented feed on the gut microbiota of different animals

摘要:

肠道微生物群落是调控动物健康的关键因素，其结构和功能可被发酵饲料显著影响。然而，目前缺乏跨物种比较研究，限制了对发酵饲料共性调控机制的理解。目的 整合多物种数据，解析发酵饲料对肠道菌群的跨物种调控规律，揭示功能优化的普遍性与宿主特异性机制。方法 整合猪、牛、鸡、鹅的464个肠道微生物组数据，分别采用α/β多样性、线性判别效应分析(linear discriminant analysis effect size, LEfSe)、BugBase及网络分析，评估发酵饲料组和对照组间的肠道微生物多样性、差异菌属、潜在致病性和互作关系。结果 发酵饲料显著降低了单胃动物(猪、鸡、鹅)肠道微生物的α多样性；不同动物肠道微生物群落的β多样性无显著变化，但发酵饲料组显著富集益生菌[如乳杆菌属(Lactobacillus)和粪杆菌属(Faecalibacterium)]，抑制了致病菌[如弯曲杆菌属(Campylobacter)、短螺菌属(Brachyspira)]，潜在致病性降低。网络分析显示发酵饲料组的连接度、网络密度提高，模块化降低，群落协同性增强。物种特异性分析表明，猪、牛、鸡分别富集了乳杆菌属(Lactobacillus)、阿克曼氏菌属(Akkermansia)、解黄酮菌属(Flavonifractor)等不同的益生菌，体现了宿主特异性响应。结论 发酵饲料通过共性响应优化结合物种特异性响应模式调控肠道菌群，选择性富集关键菌群以增强特定功能、降低致病性，为发酵饲料共性技术的开发提供理论依据。

Abstract:

The gut microbiota plays a pivotal role in regulating animal health, and its structure and function can be significantly modulated by fermented feed. However, the lack of cross-species comparative studies has hindered a comprehensive understanding of the universal mechanisms underlying fermented feed-mediated microbial regulation.Objective To integrate multi-species data for deciphering cross-species regulatory patterns of fermented feed on gut microbiota and elucidating universal functional optimization and host-specific mechanisms.Methods We aggregated 464 gut microbiome datasets from pigs, cattle, chickens, and geese. The alpha/beta diversity analyses, linear discriminant analysis effect size (LEfSe), BugBase, and network analyses were employed to assess the diversity, differentially enriched genera, pathogenicity, and interactions of the gut microbiota.Results Fermented feed markedly reduced the alpha diversity of gut microbiota in monogastric animals (pigs, chickens, and geese) but not in ruminants (cattle). Although the beta diversity of gut microbiota remained statistically stable in different animals, fermented feed enriched probiotics (e.g., Lactobacillus and Faecalibacterium) while suppressing pathogens (e.g., Campylobacter and Brachyspira) to significantly diminish the pathogenic potential. Network analysis revealed enhanced connectivity, increased network density, reduced modularity, and improved community synergy in fermented feed groups. Host-specific responses were identified: Lactobacillus dominated in pigs, Akkermansia in cattle, and Flavonifractor in chickens.Conclusion Fermented feed modulates gut microbiota through a pattern coupling consistent response optimization with host-specific responses, selectively enriching keystone taxa to improve the specific function and reduce the pathogenicity. This study provides theoretical foundations for developing host-tailored fermented feed strategies.