Host and anatomical filters prevent microbiome convergence in avian scavengers

How host-associated microbiomes assemble under intense environmental microbial exposure remains a central question in microbial ecology. Vultures represent a unique natural system because these species differ markedly in feeding ecology and carcass use. We characterized bacterial communities across four anatomical niches (facial, buccal, tracheal, and cloacal) in 155 individuals spanning all four European obligate vulture species (subfamily Gypaetinae: Gypaetus barbatus, Neophron percnopterus, and Aegypiinae: Aegypius monachus and Gyps fulvus ) and the facultative scavenger Milvus milvus . Microbiome composition was jointly structured by host species and anatomical niche, with host identity explaining more variation than anatomical compartment and a significant interaction indicating that interspecific differentiation depended on body site. Each niche supported distinct bacterial assemblages and core microbiomes: Cloacal communities were enriched in anaerobic gut-associated taxa, whereas facial and tracheal communities contained more environmental and respiratory-associated bacteria. Host-specific taxonomic signatures persisted within anatomical niches despite recurrent exposure to the same carrion-associated microbial pool. Age further influenced community composition, whereas sex had little detectable effect. The facultative scavenger showed the same broad anatomical compartmentalization observed in obligate scavengers, although taxonomic signatures differed among species. Thus, sustained exposure to a shared, microbially rich resource was insufficient to produce a common scavenger microbiome. Instead, microbiome assembly reflected hierarchical filtering by host identity, anatomical environment, and ontogeny. These findings distinguish microbial exposure from microbial persistence, establishing avian scavengers as a natural model for understanding how host-associated communities remain differentiated, despite recurrent exposure to shared environmental microbial reservoirs across ecological and anatomical scales in vertebrate hosts.