Convergent Gut Microbiome Adaptation and Pervasive Antibiotic Resistome in Qinghai‒Tibet Plateau Passerines

Metagenomic analysis of nonmigratory passerines (Pseudopodoces humilis and Pyrgilauda ruficollis) and their habitats on the Qinghai‒Tibet Plateau revealed convergent adaptations in gut microbial composition and function dominated by Bacillota and Pseudomonadota. Functional enrichment in carbohydrate metabolism and genetic information processing underpins host energy optimization in extreme high-altitude environments. Critically, these birds constitute a major reservoir of antibiotic resistance genes (ARGs), harbouring 162 antibiotic resistance ontologies (AROs) with nearly universal resistance to clinical antibiotic classes. The core resistome—comprising glycopeptide (van clusters), fluoroquinolone, and tetracycline resistance genes—reflects anthropogenic contamination amplified by environmental persistence. Environmental transmission pathways were unequivocally demonstrated via 53 AROs shared between avian hosts and proximal matrices (soil/grass), coupled with livestock-derived antibiotic influx through excreta, establishing the plateau as a hotspot for resistance gene flux. Strikingly, "low-abundance-high-resistance" taxa (Pseudomonadota, Actinomycetota, and Bacillota; ≤20% abundance but >90% ARG contribution) drive resistome plasticity, potentially facilitated by horizontal gene transfer. Our findings redefine resident passerines as sentinels of ecosystem health and bridges for cross-boundary antimicrobial resistance (AMR) spread. Mitigating global AMR thus necessitates interdisciplinary strategies targeting environmental reservoirs (e.g., regulating livestock antibiotic use) and monitoring avian-mediated gene flow.