Bacterial populations exhibit significant heterogeneity, allowing distinct cell subgroups to thrive in diverse environments. This environmentally organized heterogeneity prompts bacteria to respond to dynamic changes through unique transcriptional programs, posing substantial challenges in assaying individual cells uniformly. Recent advancements in single-cell techniques, particularly single-cell RNA sequencing (scRNA-seq), offer a powerful means to unravel cellular heterogeneity during infections and discern subpopulation variations that influence individual cell outcomes. However, current bacterial scRNA-seq methods suffers from low number of cells being sequenced and low number of transcripts detected in each cell due to leakage of nucleic acids due to mechanical disruption of cell wall during permeabilization for subsequent enzymatic reactions. Therefore, we are developing a novel bacterial scRNA-seq method by using advantage of semi-permeable hydrogel microcapsules (SPCs), which allows encapsulation of bacterial cells by microfluidics device and multiple enzymatic reactions once the cells are lysed inside SPCs.