The complex diversity of microbial communities is a remarkable feature of the biological world, carrying vast fundamental and economical potential. Understanding the complex dynamics within these communities is a challenging task, yet it offers opportunities to discover new biological mechanisms, unearth valuable bioproducts, and create innovations. Driven by this challenge, the goal of this PhD project is to establish the single-cell technology for high-throughput microorganism transcriptomics of microorganisms. We will leverage microcapsule-based technology that combines the key advantages of droplet microfluidics and combinatorial indexing by split-pool to barcode transcriptome (or genome) of single cells with a very high efficiency. We will apply the advanced technology and tools to investigate how bacteria develops antibiotic resistance. The potential impact of PhD research is immense and extends well beyond the confines of microbiology. With the alarming rise in antibiotic-resistant microorganisms, the findings of the PhD work could pave the way for novel treatments and strategies to combat these resistant strains and spur new innovations. Dissecting heterogeneous populations down to individual cells along with their transcriptional response will provide us an opportunity for deepen our fundamental insights into the biological mechanisms underpinning microbial drug resistance, pathogenesis and others.