In addition to the focus on microbial effectors, metaproteomics is an important method for monitoring microbiomes and implementing strategies for controlling them. As shown in several studies, metaproteome is very predictive of temporal variations within microbiomes [139] and hence a crucial indicator of how/when one can intervene for example by altering substrate availability, physico-chemical parameters or by CRISPR-based community-wide engineering/editing . In clinical settings, metaproteomics provides valuable insights into the current state of a patient's microbiome, facilitating the identification of dysbiosis and the prediction of drug-microbiome interactions. This approach also enables continuous monitoring of therapeutic progress.