Pellets were thawed on ice and resuspended in RNAase free water, 50 mL of 0.1 mm silica spheres (MP Lysing Matrix B) were added, and samples were bead-beaten for 90 seconds in three intervals at 4°C. Total RNA was then extracted using the MasterPure Complete RNA Purification kit (Lucigen). Genomic DNA was removed using the Turbo DNA-free kit (Ambion). Total RNA was measured with an Agilent 2100 Bioanalyzer (Agilent Technologies). The libraries were prepared using the Ribo-Zero Magnetic Kit (Bacteria; Epicentre) and the KAPA RNA HyperPrep kit (Kapa Biosystems). Library sequencing was performed using the Illumina HiSeq 2000 platform with a single-end protocol and read lengths of 40 nucleotides. Samples were stored at -20°C. Total RNA (depleted of rRNA) was converted to cDNA and sequenced with Illumina HiSeq 2000 with a single-end protocol and read lengths of 40 nucleotides