In conclusion, the proportion of the active microbiome that can be measured by state-of-the-art metaproteomics experiments holds immense potential in the clinical context, with significant progress being made in understanding its role in various diseases . Despite promising results, unraveling the causal contributions of microbiome traits to host biology and translating microbiome-based biomarkers into clinical practice remains significantly challenging. Non-model gut commensals encode many traits, and the sample size in omics studies often lacks the power needed for functional monitoring of the microbiome in clinical contexts. Additionally, advancing the microbiome's clinical applications will require further well-designed clinical trials and the integration of multidisciplinary approaches. Metaproteomics, complemented with bioinformatics and machine learning, represents an essential toolbox for untangling the complex interactions between microbiome components and host health, thereby paving the way for novel therapeutic strategies. In this respect first assays for studying the drug response of microbiomes combined with metaproteomics were tested [130], highlighting the potential of pharmacomicrobiomics.