Abstract
Microbial communities are fundamental to host health, yet their assembly dynamics under environmental change remain poorly understood. We analysed individual-level host-microbe networks in the non-native wild black rats (Rattus rattus) across a land-use gradient in Madagascar. By applying a moving prevalence threshold, we distinguished between core and non-core microbes and compared the assembly drivers shaping their network structures. Non-core microbes formed fragmented, modular networks shaped mainly by heterogeneous selection, reflecting environmental filtering. In contrast, core microbes exhibited stable, less modular networks driven primarily by stochastic ecological drift. These distinct assembly processes persisted across thresholds, highlighting fundamental differences in microbial structuring. Land-use change significantly influenced the modular structure of non-core microbes but had minimal effects on core microbes, demonstrating the differential sensitivity of microbial groups to environmental variation. This study advances our understanding of host-microbe interactions and provides a framework for assessing microbiome assembly under anthropogenic change.