Subcellular compartmentalization is a fundamental characteristic of life that helps cells to regulate their metabolism in time and space, carry out specialized metabolic reactions, prevent toxicity, and store nutrients. As prokaryotes generally do not possess membrane organelles, they have to rely on protein-based approaches to compartmentalize their cytoplasm. Protein organelles are nano-sized functional analogues of eukaryotic membrane organelles and utilize a semipermeable protein shell to create a sequestered space separated from the rest of the cell. This compartmentalization strategy can increase the local concentrations of enzymes and metabolites, prevent the leakage of toxic or volatile intermediates, and create unique microenvironments with regard to pH and redox state. Protein organelles enable specialized biochemistry that would not be possible without compartmentalization. Protein organelles are present in nearly all bacterial and archaeal phyla and can be found in many important human commensals and pathogens. Protein organelles have been suggested to increase bacterial stress resistance, allow the utilization of alternative nutrients, and help bacteria to colonize the human host. The two main classes of microbial protein organelles are encapsulin nanocompartments (20-50 nm) and bacterial microcompartments (40-200 nm). In both cases, specialized enzymatic machinery is selectively encapsulated within self-assembling protein shells leading to unique catalytic capabilities. The overall goal of my laboratory is to explore and understand the functional diversity of protein organelles encoded in microbial genomes. Thousands of commensal and pathogenic bacteria encode encapsulins or BMCs which have been proposed to increase bacterial fitness and adaptability in dynamic environments. However, the structures, molecular mechanisms, and physiological functions of most protein organelles have not been explored while their contributions towards human health and disease are poorly understood. To change this, we will prioritize four research areas, focusing on protein organelle (1) structure and enzymology, (2) contribution towards stress resistance, (3) role in nutrient utilization and metabolism, and (4) involvement in secondary metabolite biosynthesis. We will use a multifaceted strategy relying on biochemistry, structural biology, and microbiology approaches. Our findings will provide novel biochemical, structural, and physiological insights into the role of protein-based compartmentalization in bacteria and help elucidate how protein organelles contribute towards the fitness of both commensal and pathogenic bacteria. This information will be essential for exploring future therapeutic avenues aimed at disrupting protein organelle function and utilizing protein organelles for biomedical applications.