Cells were cultured in TSBT broth to OD600 ~ 0.8. Total RNA was isolated using bead beating with Trizol. Ribosomal RNA was depleted with NEBNext rRNA Depletion Kit for bacteria supplemented with mycospike probe mix. The rRNA-depleted RNAs were processed using the NEBNext Ultra II Kit. Over 10 M reads paired-0end reads were obtained.