RNAseq of bacterial synthetic community at day5 rep1
For the RNA sequencing, the SynCom was propagated in the artificial soil matrix and challenged with either B. subtilis P5_B1 or the mutant impaired in NRP synthesis (sfp mutant). A SynCom without B. subtilis inoculation served as the control group. The RNA extraction was performed using the RNeasy.  Reads were trimmed using trimmomatic v.039. PowerSoil Total RNA Kit (QIAGEN) following the manufacturers instructions. After extraction, the samples were TURBODNA-free kit (ThermoFisher) to degrade the remaining DNA.  Reads were demultiplxed by the sequencing company. Quality was assessed with FASTQC and read were sorted with Sort MeRNA v.4.2.0. Reads were mapped onto the genomes of each SynCom member using Bwtie v.2-2.3.2. Diffential gene expression analysis was conducted in DESeq2 in R.
SUB14619124
SynCom5_1