A metaproteomic platform for integrated host-pathogen-microbiota profiling in zebrafish larvae

Understanding host-pathogen-microbiota interactions requires analytical strategies capable of resolving multiple biological compartments within a single experimental framework. Here, we present a global metaproteomic workflow that enables the simultaneous profiling of host, pathogen and endogenous microbiota from complex infection samples. Using zebrafish larvae infected with Pseudomonas aeruginosa as a demonstrative model, we show that peptide-centric metaproteomic analysis provides integrated taxonomic and functional resolution across all components of the system. The approach captures route-dependent differences in microbial representation, community restructuring and functional activation, while concurrently reporting host proteome remodeling. This work establishes metaproteomics as a versatile analytical platform for dissecting host-pathogen-microbiota systems in vivo and highlights its potential for studying complex infection-driven biological networks within a unified proteomic framework.