Integrative analysis of rumen microbiome and host metabolism reveals adaptive strategies of Boer goats to high-altitude environments.

The transition to high-altitude environments presents significant metabolic challenges for livestock, primarily due to hypoxia and altered dietary resources. Understanding the adaptive strategies involving the rumen microbiome and host metabolism is crucial for improving animal health and productivity in these regions. This study investigated the adaptive responses of Boer goats to high-altitude exposure by integrating ruminal fermentation, ruminal and fecal microbiota, and serum metabolomics. The results demonstrated that high-altitude exposure markedly reshaped ruminal fermentation, microbiota composition, and serum metabolome of Boer goats. Concomitant with the elevational shift, the ruminal pH increased, whereas acetic acid concentration and the acetate-to-propionate ratio decreased; however, fecal volatile fatty acid concentrations remained unchanged. Microbial alpha diversity was reduced in both ruminal and fecal samples. The high-altitude rumen of Boer goats was characterized by an enrichment of fiber-degradation-associated taxa, accompanied by significantly elevated relative abundances of Firmicutes_A, Ruminococcus_E, as well as a heightened Firmicutes-to-Bacteroidetes ratio; in contrast, the relative abundances of fecal Patescibacteria, Faecousia, and Phocaeicola_A were decreased. Serum metabolomics profiling revealed that the acclimatization of Boer goats to high altitudes was characterized by profound alterations in energy and amino acid metabolism, coupled with hydromineral regulation and neuroactive metabolite pathways. Notably, energy-related metabolites, including 2-oxoglutaric acid, 3-hydroxybutyric acid, and L-malic acid, were elevated in the high-altitude cohort and positively correlated with fibrolytic taxa such as Fibrobacterota, Fibrobacter and Ruminococcus_E. In summary, the metabolic synergy between the rumen microbiome and the host likely contributes to maintaining energy homeostasis in Boer goats in high-altitude environments. These findings provide a useful reference for developing targeted nutritional strategies to improve goat farming in plateau regions.