The gut microbiota composition is influenced by the diet as well as the environment in both wild and domestic animals. We studied the effects of two feeding systems on the rumen and hindgut microbiome of semi-feral Tibetan goats kept at high altitude (∼4800 m) using 16S rRNA gene and metagenomic sequencing. Intensive drylot feeding resulted in significantly higher zootechnical performance, narrower ruminal acetate: propionate ratios and a drop in the average rumen pH at slaughter to ∼5.04. Hindgut microbial adaption appeared to be more diverse in the drylot group suggesting a higher influx of undegraded complex non-starch polysaccharides from the rumen. Despite their higher fiber levels in the diet, grazing goats exhibited lower counts of Methanobrevibacter and genes associated with the hydrogenotrophic methanogenesis pathway, presumably reflecting the scarce dietary conditions (low energy density) when rearing goats on pasture from extreme alpine environments. These conditions appeared to promote a relevant abundance of bacitracin genes. In parallel, we recognized a significant increase in the abundance of antibiotic resistance genes in the digestive tracts of drylot animals. In summary, this study provides a deeper insight into the metataxonomic and functional adaption of the gastrointestinal microbiome of goats subject to intensive drylot and extensive pasture rearing conditions at high altitude.

中文翻译：

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在高强度或广泛饲养条件下保持在高海拔（4800 m）的山羊胃肠道微生物组的分类和功能适应

肠道微生物群的组成受饮食以及野生和家养动物环境的影响。我们使用16S rRNA基因和宏基因组测序研究了两种饲喂系统对高海拔（〜4800 m）的半野生藏山羊的瘤胃和后肠微生物组的影响。密集的干法饲喂可显着提高动物技术性能，瘤胃乙酸：丙酸瘤胃比例变窄，屠宰时瘤胃的平均瘤胃pH值下降至约5.04。干羊群的后肠微生物适应性似乎更多样化，表明瘤胃中大量未降解的复合非淀粉多糖大量涌入。尽管日粮中的纤维含量较高，但放牧山羊的甲烷短杆菌数量较少以及与氢营养型甲烷生成途径相关的基因，大概反映了从极端高山环境中在牧场上饲养山羊时饮食条件的稀缺（低能量密度）。这些条件似乎促进了杆菌肽基因的相关丰度。同时，我们认识到干场动物消化道中抗生素抗性基因的丰度大大增加。总而言之，这项研究提供了对山羊胃肠道微生物组的元分类学和功能适应性的更深入了解，山羊在高海拔地区需要大量的干法饲养和广泛的牧场饲养条件。