The microbiome—a complex and dynamic community of bacteria, viruses, archaea, and fungi occupying distinct functional niches—is deeply intertwined with both physiological and pathophysiological processes. There is virtually no aspect of human biology that remains untouched by its influence. Although our understanding of key compositional and functional aspects of the gut microbiome has expanded dramatically over the past two decades, many critical questions remain unanswered. Our research group is particularly focused on the clinical relevance of the gut microbiome, exploring how it impacts disease trajectories and influences treatment outcomes.