Emerging single-cell microfluidic technology for microbiology

Cell-to-cell differences exist ubiquitously in microbial communities. This individual heterogeneity, often manifested in cell phenotypic function (e.g., antibiotic resistance), can be critical in determining the fate of a microbial community. However, studying such heterogeneity in microbial communities remains a significant challenge due to their enormous diversity and complex cell-cell interactions. Here we review recent advances in microfluidic technologies for detecting, manipulating, and sorting microbial populations at the single-cell level, which significantly advanced our understanding of microbial behaviour and their roles in the microbial ecosystem. We will highlight microfluidic systems with label-free detection methods, including optical imaging and Raman spectroscopy, due to their advantages in investigating real-world microbial communities. We will showcase these technologies in emerging applications, including rapid diagnosis of pathogens and antibiotic resistance, chemotaxis, and Raman-activated cell sorting to search for natural microbial cells of desirable phenotypic function.