Bacterial Inoculation via Gastric Gavage

Cr strain, DBS100 (ATCC) was used for scRNA-seq experiments. For flow cytometry analysis and to track Crin situ, we used a strain of Cr expressing GFP^{61 (link)} (derived from DBS100; provided by B. A. Vallance). For whole-body imaging experiments, we used the bioluminescent Cr strain ICC180⁶² (derived from DBS100; generously provided by G. Frankel and S. Wiles). A fresh, single colony was grown in 10 ml LB at 37 °C with rotation at 225 rpm for 12–14 h. Next day, 1 ml of overnight culture was added to 250 ml LB broth, incubated at 37 °C with rotation (225 rpm) for 3–3.5 h until OD₆₀₀ reached 1.0 on spectrophotometer. Bacteria were pelleted at 25 °C, 3,000 rpm for 15 min and then resuspended in 5 ml sterile PBS. Mice were inoculated with 2 × 10⁹ CFU in a total volume of 100 µl of PBS by gastric gavage.