Coping with extremes: diet and phylogeny shape gut microbiota in six passerine species inhabiting the Qinghai-Tibet Plateau

Understanding how diet and host phylogeny shape gut microbiota is fundamental to elucidating host-microbe interactions in extreme environments. The Qinghai-Tibet Plateau (QTP), characterized by harsh conditions, provides a natural laboratory for examining these relationships among sympatric species. Here, we investigated the dietary composition and gut microbiota of six passerine species inhabiting the QTP, comprising two endemic residents (White-rumped Snowfinch Onychostruthus taczanowskii and Ground Tit Pseudopodoces humilis), two non-endemic residents (Rock Sparrow Petronia petronia and Eurasian Tree Sparrow Passer montanus), and two non-endemic migratory species (Twite Linaria flavirostris and Black Redstart Phoenicurus ochruros), using high-throughput 18S and 16S rRNA sequencing. Our results revealed that dietary composition—dominated by Archaeplastida, Metazoa, Fungi, and the SAR supergroup—exhibited no significant interspecific variation, reflecting a high degree of trophic niche overlap. Although the overall diet was similar across species, the relative abundances of certain dietary components independently influenced specific microbial taxa. In particular, dietary Archaeplastida and Fungi showed phylogeny-independent positive correlations with 16 and 3 microbial genera, respectively, revealing fine-scale diet-microbiota associations. Evidence of phylosymbiosis was detected, as closely related species harbored more similar microbial communities driven by species-specific microbial biomarkers. Notably, our results suggested deterministic processes played a stronger role in endemic species, whereas stochastic community assembly dominated in non-endemic species, indicating distinct assembly mechanisms shaped by biogeographic history. Overall, this study reveals that while dietary similarity promotes convergent trophic niches among sympatric passerines, host phylogeny exerts a stronger influence on gut microbiota composition and assembly. These findings underline the synergistic roles of diet-microbiota interactions and phylosymbiosis dynamics as key adaptive strategies that enable birds to cope with the extreme environments of the QTP.