hi @Netanel_Cohen
stringency of trimming depends on downstream analysis, so take settings from a recent paper with a similar analysis as yours or test different trimming setups on one sample or small number of samples. Number of reads is not really relevant without information on the project. 47M reads look like an overkill for differential gene expression in bacteria but might not be sufficient for whole genome variant calling, and excessive data might results in poor quality in some projects.
Kind regards,
Igor