Lb broth

Escherichia
coli strains used for this study are listed in Table 4. SN1171, SN1187,
BL21(DE3), and DH5α were used for the recipient strains for
transduction. SN1187 was used as the ΔrecA strain.
For homemade packaging extract preparation, SN2099 or SN2100 was used.
These strains were constructed by knocking out the region from the SRRz gene to the cos site of the λ phage genome integrated
into the attλ site of the host strain by the method of Datsenko
and Wanner.^{43 (link)} LB broth (1% trypton, 0.5%
yeast extract, 1% NaCl) (Nacalai Tesque) was used for liquid culture.
The agar plates were made by adding 1.5% agar to LB broth. Then, 50
μg/mL ampicillin was added to the medium when antibiotic resistance
selection was needed. MgSO₄ with a final concentration
of 10 mM and 0.7% agar were added to LB broth to make soft agar for
plaque assay.

BL21(DE3) was purchased from Novagen. The LB broth (Miller) was purchased from Nacalai Tesque (Japan), the M9 minimal salts premix was purchased from MP Biomedical Japan, and the 2-YT broth was purchased from Invitrogen. The glycerol minimal medium containing l-leucine (GMML)26 (link) in our study consisted of M9 minimal medium, 1 mM MgSO₄, 1% glycerol, 0.3 mM l-leucine, and Kao and Michayluk vitamin solution (Sigma-Aldrich). The GMML auto-induction culture for the HV1 preparation consisted of 0.05% d-glucose, 0.2% d-lactose, 0.5% glycerol, NSP, vitamins, 10 mM O-sulfo-l-tyrosine (Watanabe Chemical Industries, Hiroshima, Japan), and carbenicillin (100 μg/ml). The auto-induction medium for the Fab preparation consisted of 2-YT, 1 mM MgSO₄, 0.05% d-glucose, 0.2% d-lactose, 0.5% glycerol, nitrogen sulfur phosphorus solution (NSP), 1 mM azido-l-phenylalanine (Bachem), and kanamycin (30 μg/ml). The 20-fold concentrated NSP solution (pH6.8) was composed of 0.5 M KH₂PO₄ (68 g), 0.5 M Na₂HPO₄ (71 g), 1 M NH₄Cl (53.6 g), and 0.1 M Na₂SO₄ (14.2 g) per liter. Anaerobic culturing was performed using Culture set, FX-2 (ISO, Japan). The optical cell densities were measured with an Ultraspec spectrophotometer (GE Healthcare) and Libra S11 Visible and UV spectrophotometers (Biochrom Ltd.).

N. meningitidis strains HT1125 and its derivatives, and H44/76 and its derivatives were stored at −80°C, and routinely grown on GC agar plates at 37°C in 5% CO₂ [47 (link), 48 (link)]. E. coli strains BL21-Gold(DE3), BW25113, and JW4107 (BW25113 Δefp) were grown on plates or liquid culture of LB broth, Miller (Nacalai Tesque) at 37°C.

Escherichia coli K12 ATCC10798, purchased from the American Type Culture Collection (ATCC), was used as the non-AIEC strain. E. coli LF82 strain was isolated from a chronic ileal lesion in a patient with CD and used as the AIEC strain [32 (link)]. The following clinical isolates of E. coli were used in this study: E. coli HS, LF1, LF6, LF19, LF48, LF55, LF111, LF134, LF135, LF82, LF16, LF31, LF73, 6076, 6088, 6170, 6254, 6259, and 6283 [33 (link), 34 (link)]. All bacteria were routinely cultured in LB broth (Nacalai Tesque Inc., Japan) overnight at 37 °C with shaking at 160 rpm until their growth reached the mid-exponential phase (OD₅₇₀ = 1.0).
Human colon adenocarcinoma, Caco-2, cells were purchased from the European Collection of Cell Cultures (ECACC 86010202). Caco-2 cells were maintained in a 5% CO₂ atmosphere at 37 °C in DMEM (Gibco), supplemented with 10% (v/v) fetal bovine serum (Gibco), 0.01% minimum essential medium non-essential amino acids solution (Invitrogen), 0.01% L-glutamine (Invitrogen), and 0.01% penicillin–streptomycin (Nacalai Tesque Inc.).