Bacto tryptone

Pseudomonas oleovorans NRRL B-14682, Pseudomonas oleovorans NRRL B-14683, Pseudomonas citronellolis NRRL B-2504, a new isolate of Pseudomonas sp., and Burkholderia thailandensis E264 were used in this study. Luria–Bertani (LB) broth (Bacto tryptone (Fisher Scientific, Hampton, NH, USA), 10 g/L; yeast extract (Biolife, Bothell, WA, USA), 5 g/L; sodium chloride (Fisher Scientific, 99.5%), 10 g/L, pH 6.8) was utilised for the inoculum preparation, while Medium E* supplemented with the enzymatic hydrolysate was used for the cultivation assays. The composition (per litre) of the Medium E* was as follows: (NH₄)₂HPO₄, 1.1 g; K₂HPO₄, 5.8 g; KH₂PO₄, 3.7 g; 10 mL of a 100 mM MgSO₄ solution; and 1 mL of a micronutrient solution [9 (link)]. The composition of the micronutrient solution (per litre of 1 N HCl) was as follows: FeSO₄⋅7H₂O (Sigma-Aldrich, St. Louis, MO, USA), 2.78 g; MnCl₂⋅4H₂O (Sigma-Aldrich), 1.98 g; CoSO₄⋅7H₂O (Sigma-Aldrich), 2.81 g; CaCl₂⋅2H₂O, 1.67 g; CuCl₂⋅2H₂O (Sigma-Aldrich), 0.17 g; and ZnSO₄⋅7H₂O (Sigma-Aldrich), 0.29 g. The pH of the media was set to 7.0 by the addition of NaOH prior to autoclaving at 121 °C and 1 bar for 20 min.

The E. coli strains and their mutants used in this study are listed in Table 1. Whole-genome sequences of the 442 O121:H19 strains (Data set S1) previously used in our phylogenetic analysis (13 ) were used for the analysis of IS insertion into the lacZ and iee genes.
Bacteria were grown in the following media: LB (1% [wt/vol] Bacto Tryptone, Gibco; 0.5% [wt/vol] Bacto Yeast Extract, Becton, Dickinson [BD]; 1% [wt/vol] sodium chloride, nacalai tesque), LB agar (LB containing 1.5% [wt/vol] Bacto Agar, BD), MAC (Difco MacConkey agar base, BD; 1% [wt/vol] lactose monohydrate, Wako), MAC not supplemented with lactose (Difco MacConkey agar base), Pearlcore MAC (Pearlcore MacConkey agar, Eiken Chemical Co.), MM (Difco M9 Minimal Salts, BD; 2 mM magnesium sulfate heptahydrate, Wako; 0.1% D-[+]-glucose, nacalai tesque), and MM agar (MM containing 1.5% [wt/vol] Bacto Agar). The growth media were supplemented with regents and antibiotics when necessary at the following concentrations: L(+)-arabinose (Wako), 1 mM; IPTG (Wako), 0.3 mM or 30 mM; X-gal (TaKaRa), 40 μg/mL; sucrose (nacalai tesque), 10% (wt/vol); D-(+)-glucose, 0.1%, 0.2%, or 0.4% (wt/vol); lactose monohydrate, 1.0% (wt/vol); D(+)-maltose monohydrate (Wako), 1.0% (wt/vol); chloramphenicol (Wako), 20 μg/mL; ampicillin (Sigma), 50 μg/mL; tetracycline (nacalai tesque), 10 μg/mL.

Cells were cultured overnight in liquid Luria Broth (LB) medium at 30°C, and then, 10 ml of the cell culture was inoculated into 1 l of modified Terrific Broth (TB) medium (per liter: 12 g Bacto Tryptone; Gibco), 24 g Bacto yeast extract, 9.4 g K₂HPO₄, 2.2 g KH₂PO₄ and appropriate antibiotics (100 mg spectinomycin, 10 mg tetracycline and 30 mg chloramphenicol). Cultures were grown at 25°C in a 3-l jar fermenter (BMJ-03P, ABLE). The pH was maintained at 7.0 by automatic addition of 28% NH₄OH and 25% H₃PO₄. The agitation speed was 100 rpm. At the time of inoculation, dissolved oxygen levels were allowed to fall to 10% of O₂ saturation with a continuous air supply of 1 volume per minute. The glucose concentration was maintained at 0.4 g/l by the addition of 15% (w/v) glucose solution. 0.1 mM IPTG and 0.1% (v/v) ethyl 3-oxobutanate were then added to the culture when Optical Density at 600 nm (OD₆₀₀) reached 10.

Salmonella enterica subsp. enterica sv. Typhi strain STH2370 (S. Typhi) was used as the parental strain (Valenzuela et al., 2014 (link)). The strain was routinely grown in liquid culture using Luria Bertani medium (Bacto tryptone [Gibco], 10 g/L; Bacto yeast extract [Gibco], 5 g/L; NaCl [Winkler], 5 g/L; prepared in distilled water) at 37°C with shaking. When required, the medium was supplemented with agar (15 g/L), ampicillin (Amp, AppliChem GmbH), polymyxin B sulfate (Pmb, AppliChem GmbH), or meropenem (Mer, Sigma Aldrich). For S. Typhi, 1× Amp represents a concentration equivalent to the Minimum Inhibitory Concentration (MIC) of Amp (6.25 μg/mL), while 1× Pmb corresponds to the MIC of polymyxin B (0.31 μg/mL). Various concentrations based on these standards were employed, such as 0.25× Amp (1.56 μg/mL), 0.5× Amp (3.13 μg/mL), 2× Pmb (0.63 μg/mL), and 4× Pmb (1.25 μg/mL).