metatranscriptomics of B. fragilis
Total RNA was extracted using ZymoBIOMICS DNA/RNA miniprep kit following the manufacturers instructions (Zymo). Following extraction, libraries were prepared for sequencing using the KAPA RNA HyperPrep kit (Roche). Libraries were quality assessed using Qubit dsDNA, high sensitivity (ThermoFisher, Cat# Q32851) and a Bioanalyzer (Agilent Technologies) and subsequently sequenced on the paired-end NovaSeq PE 100 V2 kit (Illumina). Transcriptomic reads were trimmed using Trim Galore v0.6.10 paired-end mode with default parameters and aligned to the reference database Web of Life using bowtie2 v2.2.5. Taxon count tables were generated from alignment using Woltka v0.1.5.