Although metaproteomics is a powerful tool for studying microbiomes and microbial effectors, its potential is greatly enhanced by integrating additional omics approaches (Figure ). Cytomics enables monitoring and sorting microbial subpopulations, providing insights into cell-specific behaviors. Furthermore, cytomics can measure cell viability , which is of great importance e.g., to assess the response of microbiomes to antimicrobials and could even provide the potential to evaluate community structure, diversity, and metabolite exchange in response to microbial effectors [100]. Metagenomics is essential for generating sample-specific databases used in protein identification, while predicted genes from metagenomic data serve as input for taxonomic and functional characterization (e.g., antibiotic production or resistance) using sequence alignment tools. Metagenomics typically offers higher resolution, allowing for more detailed insights into the taxonomic and functional composition of the microbiome. It also enables a unique opportunity to study operon structures and surrounding genes as well as the encoding of microbial effectors in the genome or in mobile genetic elements . Liquid