In one experimental outline of the Swiss Webster study the mice were fed on the same day and analysed on different days post-treatment. In the second experiment mice were fed on days 3, 7 and 14 prior to the analysis and mice were then all analysed on

the same day. Both experimental designs check details yielded results that were indistinguishable; therefore, data from both Swiss Webster experiments were combined. The experiment with 129/SvEv mice was staggered so that mice belonging to one experimental time-point group were analysed on two different days. Mice were killed by cervical dislocation prior to faecal slurry inoculation (axenic) and on days 3, 7, 14 and 28 post-inoculation. Colon, caecum and ileum were excised, cut longitudinally and half of each organ was prepared in paraffin with haematoxylin and eosin staining for light-microscopic examination as detailed previously [8]. The slides were reviewed in a blinded fashion and were assigned a histological score for intestinal inflammation ranging from 0 (no injury) to 10 (maximal injury). The histological inflammation scale represents the numerical sum of four scoring criteria: mucosal ulceration, epithelial hyperplasia, lamina propria mononuclear infiltration and lamina propria MK-2206 clinical trial neutrophilic infiltration [8]. To study epithelial barrier function a segment of colon was assayed in Ussing chambers,

as described previously [9]. In the chambers the flux of [3H]-labelled mannitol from the mucosal to the serosal side was monitored as an indicator for the permeability of the intestinal epithelial layer. Parts of colon, caecum and ileum were cultured for 24 h in 1 ml complete RPMI-1640 medium, as described previously [8]. Cytokine release in the supernatants was quantified using standard sandwich ID-8 enzyme-linked immunosorbent assay (ELISA) techniques. For the ELISA the following antibodies were used: anti-interferon (IFN)-γ (clone R4-6A2), anti-tumour necrosis factor (TNF)-α (clone G281-2626), anti-interleukin (IL)-17 (clone eBioTC11-18H10·1),

anti-IL-10 (clone JES5-2A5) and anti-IL-4 (clone 11B11) as capture antibodies and biotinylated anti-IFN-γ (clone XMG1·2), anti-TNF-α (clone MP6-XT3), anti-IL-17 (clone eBioTC11-8H4), anti-IL-10 (clone JES5-16E3) and anti-IL-4 (clone BVD6-24G2) as detection antibodies. All antibodies and recombinant cytokine standards were purchased from PharMingen Canada (Mississauga, Ontario, Canada) except for the anti-IL-17 monoclonal antibodies, which were obtained from eBiosciences (San Diego, CA, USA). All antibodies and standards were used at pre-titred concentrations to give optimal results. For the detection of IL-6 and granulocyte-colony stimulating factor (G-CSF) commercially available kits (R&D Systems, Minneapolis, MN, USA) were used. Spleens were removed from the killed mice, minced into a single-cell suspension in complete RPMI-1640 with 10% fetal calf serum (FCS) and depleted of red blood cells by osmotic shock.