Contribution of metaproteomics to unveiling the functional role of the gut microbiome in human physiology and metabolism

Introduction: The human gut microbiome (HGM) profoundly influences human physiology. In recent years, it has become clearer that a healthy HGM is much better defined by its functional profile than by its taxonomic composition. Metaproteomics is the optimal approach to assessing the functional profile of the HGM in a taxon-specific manner, offering a direct view of its biological activity. Areas covered: First, we summarized the main wet lab and data analysis approaches used in gut metaproteomics. Next, we reviewed metaproteomic studies that have characterized the HGM of healthy adults. Lastly, we examined the functional changes induced in the HGM by specific dietary interventions. Expert opinion: Current fecal metaproteomics provides an initial understanding of the roles of gut microbes in human health, revealing redundant and taxon-specific functions. Future research should prioritize standardization, large-scale studies, and integration with multi-omics to better understand HGM metabolism. Emerging technologies, advanced mass spectrometry platforms, and AI-driven analytics are expected to increase sensitivity and depth of gut metaproteomics, accelerating discovery and potential clinical applications.