Divergent Gut Microbiota Configurations Are Associated with Contrasting Physiological Profiles in Grazing Yaks and Introduced Feedlot Holstein Cattle Under High-Altitude Conditions

The Qinghai–Tibet Plateau presents extreme environmental challenges, including hypobaric hypoxia and nutritional scarcity, to which indigenous yaks (Bos grunniens) are remarkably adapted, whereas introduced Holstein cattle (Bos taurus) often exhibit severe maladaptation. This study compared the gut microbiota of grazing yaks (n = 20) and feedlot Holstein cattle (n = 20) under high-altitude conditions using 16S rRNA gene amplicon sequencing (for community composition) and shotgun metagenomic sequencing (for direct functional profiling of CAZy, COG, and KEGG pathways), combined with in vitro fermentation, digestive enzyme assays, and serum immune- and growth-related indicators. Results: The yak gut microbiota was dominated by Proteobacteria (35 ± 4%) and Actinobacteria (15 ± 2%), whereas Holstein cattle were dominated by Firmicutes (40 ± 4%) and Bacteroidetes (25 ± 3%). At the species level, NR-based metagenomic annotation suggested that Acinetobacter-related taxa, putatively assigned as Acinetobacter pseudolwoffii and A. lwoffii, were abundant in yaks. Functional profiling revealed that the yak microbiota was enriched in CAZy families CE1, GT2, and GT4, whereas the feedlot Holstein cattle microbiota showed enrichment of several KEGG orthologs related to multidrug efflux and carbohydrate transport, including dinF/mepA/vmrA and susC/susD. In vitro fermentation using enriched culturable fecal bacterial consortia showed higher dry matter digestibility and digestive enzyme activities in yak-derived consortia than in Holstein-derived consortia. For serum immune indicators, IgG was significantly higher in feedlot Holstein cattle, whereas IgA and IgM did not differ significantly between groups. Yaks showed higher serum levels of TNF-α, IL-6, TGF-β1, IL-4, IL-10, and IL-13, but lower IL-1β. Conclusions: These findings indicate that divergent gut microbiota configurations are associated with contrasting physiological profiles (e.g., digestive and immune functions) in grazing yaks and introduced feedlot Holstein cattle under the same high-altitude environment. However, due to the confounding effects of diet and management system, causal relationships cannot be inferred from this comparative study.