Beyond microbiome monitoring, metaproteomics data can inform microbial abundance estimates, which are essential for developing control algorithms to manage microbiomes effectively . Using these algorithms, control variables such as nutrient supply, process parameters (e.g., temperature), or the introduction of microbial effectors can be adjusted to achieve the desired microbiome functionality. This concept of microbiome management is indeed in analogy to animal gastrointestinal tracts regulating their microbiomes. Closing the gap to the One Health concept, the most comprehensively studied system for microbiome management is the human gut, whose control mechanism (e.g. antimicrobial peptides) could be applied also to manage microbiomes in environment and biotechnological applications.