Protected area management contexts are associated with variation in Tibetan macaque gut microbiota and antibiotic resistomes.

Protected areas (PAs) are central to global biodiversity conservation and differ in their management contexts and associated patterns of human activity, yet differences in wildlife gut microbiota and antibiotic resistomes across PAs remain poorly understood. This study employed metagenomic analyses to compare the gut microbiota and resistomes of Tibetan macaques (Macaca thibetana) across three PAs in China with differing management contexts: Emeishan Scenic Area (EMS), where ecotourism is prominent; the Tangjiahe sector of Giant Panda National Park (TJH), where ecotourism is permitted but regulated; and Mabian Dafengding National Nature Reserve (MB), where tourist access is prohibited but livelihood-related resource use persists. Results showed that the MB population was characterized by higher gut microbial diversity and antibiotic resistance gene (ARG) abundance, with broader repertoires of potential pathogen taxa and high-risk ARGs. In contrast, potential pathogen signals in EMS and TJH were dominated by a single taxon, while EMS also showed a high-abundance signal of high-risk ARGs dominated by erm(B). Study area, gut microbiota and mobile genetic element (MGE) profiles were independently associated with gut ARG composition. This study provides a new perspective for global wildlife conservation and supports incorporating microbiota and resistome surveillance into protected-area management.