Gut dysbiosis and Escherichia coli-associated enrichment of antibiotic resistance genes in diarrheal yak calves.

Yak grazing systems are fundamental to pastoralist livelihoods on the Qinghai-Tibet Plateau (QTP), and their safe and sustainable development is essential for regional socioeconomic stability. Diarrhea is a multifactorial disease that severely impairs calf growth and may lead to mortality. In this study, we integrated second- and third-generation metagenomic sequencing with untargeted metabolomics to elucidate the underlying mechanisms and associated biosafety risks in yak calves with diarrhea. The results revealed significant gut microbiota dysbiosis in affected calves, characterized by reduced α-diversity and disrupted metabolism of arachidonic acid (AA) and its derivatives. Analysis of 1799 high-quality metagenome-assembled genomes (MAGs; ≥50% completeness and ≤5% contamination) showed a markedly increased relative abundance of Escherichia coli (16.4%) in diarrheal feces, far exceeding that observed in healthy controls. Eight assembled E. coli strains served as major reservoirs of antibiotic resistance genes (ARGs), contributing to high fecal abundances of resistance genes associated with MLS antibiotics (22.1%), bacitracin (21.7%), and β-lactams (19.9%), along with abundant mobile genetic elements (MGEs), including tnpA (21.1%) and IS91 (13.0%). Viral profiling identified E. coli as a key host for bacteriophages belonging to the families Chimeraviridae, Straboviridae, and Suoliviridae. These phages carried ARGs and MGEs that matched those detected in E. coli, potentially facilitating the dissemination of resistance through horizontal gene transfer. StrainPhlAn analysis further demonstrated that multidrug-resistant E. coli strains are widespread even among healthy calves, indicating the presence of a hidden resistome with potential for inter-individual transmission. These findings provide important theoretical guidance for managing yak calf diarrhea and offer valuable references for improving livestock production safety and mitigating antimicrobial resistance on the QTP.