Droplets were generated with MobiNova-100 (MobiDrop, A1A40001). The bacterial cell was diluted by PBS-RI and each cell was wrapped into a droplet which contained pre-amplification reagent and a gel bead linked with up to millions oligos (cell unique barcode) with MobiMicrobe Chip E Single Cell Kit (MobiDrop, S310200101) and MobiMicrobe High Throughput Microbial Single Cell RNA-seq Library Construction Kit (MobiDrop, S310300101). After encapsulation, droplets suffer light cut by MobiNovaSP-100 (Mobidrop, A2A40001) following oligos diffusion into pre-amplification mix. Then the droplets were transfered into PCR tubes for PCR reaction, in which second strand cDNA synthesis and barcoding were performed. rRNA depletion was performed with MobiMicrobe High Throughput Microbial Single Cell RNA-seq rRNA depletion kit (S310500101) and the libraries were constructed with dual index primers (MobiDrop, S310400101)