Ribopure bacteria rna isolation kit

Strains used in this study are listed in Table S1. B. thetaiotaomicron VPI-5482 was grown anaerobically overnight at 37°C in TYG medium (Betian et al., 1977 (link)) plus 200 µg/ml gentamicin. Wild-type EHEC O157:H7 strain 86–24 (Griffin et al., 1988 (link)) and its isogenic mutants (ΔqseC, ΔqseE, Δcra, ΔkdpE, ΔcraΔkdpE, ΔfusK) were grown anaerobically overnight at 37°C in LB plus 50 µg/ml streptomycin. C. rodentium strains DBS770 (λstx_2dact) and its isogenic mutant MMC01 (CRΔescN) were grown anaerobically overnight in LB plus 25 µg/ml chloramphenicol. The lysogenized, Stx-deficient C. rodentium strain DBS771 was grown in LB plus 50 µg/ml kanamycin (Mallick et al., 2012 (link)). Bt overnight culture was pelleted and concentrated 10-fold in LB. Bt was plated in a 10-fold excess over EHEC or C. rodentium to represent the composition of the intestinal microbiota. E. faecalis V583 (Paulsen et al., 2003 (link)) was grown anaerobically in LB overnight, and the overnight culture was plated at a 1:1 with EHEC. The bacteria were grown anaerobically in Petri dishes in 25 ml of pre-reduced low-glucose Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) for 6 h, unless otherwise noted, in a GasPak EZ anaerobe container (Becton Dickinson). RNA was extracted using a RiboPure Bacteria RNA isolation kit (Ambion) according to manufacturer’s guidelines.