RNA-seq in vitro culture protocol
RNA isolation. RNA from bioreactor-derived bacteria was isolated using PowerMicroBiome RNA isolation kit from MO Bio Laboratories (San Diego, CA). Subsequently RNA concentration and quality were determined by RNA electrophoresis on Agilent bioanalyzer (Santa Clara, CA). rRNA removal and library preparation. rRNA was removed using Illumina Ribo-Zero Gold Bacteria Kit (San Diego, CA). We used Illumina TruSeq Stranded mRNA Library Prep  Kit (San Diego, CA. After enrichment PCR, libraries were purified with Beckman Coulter magnetic beads (Brea, CA) and 80% ethanol wash, validated on Agilent bioanalyzer and DNA concentration was determined using Quant-iT PicoGreen dsDNA Reagent from Thermo Fisher Scientific (Eugene, OR).