In addition, samples were analyzed for SCFA, BCFA, lactate and ammonia. These values provided an indication of the balance between health-promoting and toxic products produced by the microbiota after addition of the different compounds i) separately and consecutively or ii) in combination. Analysis of (changes in) these microbial metabolites provided information on the functionality of the changes that took place in the microbiota. GSK1120212 Figure 2 Schematic representation of study design and mode of sampling. A pooled stool sample was assigned to the three study arms (Clindamycin for 7 days followed by VSL#3 for 7 days, Clindamycin + VSL#3 for 7 days, no therapy

control for 7 days). Dialysis fluid and lumen samples for metabolic analysis (SCFA, BCFA, lactate, ammonia) were collected daily, lumen samples for microbial analysis were sampled before therapy and at the end of each 7 days period. Sampling Before, during (every day at 24 h intervals) and at the

end of the fermentation experiments, samples Capmatinib were taken from the lumen of the model and from the dialysis liquid for analysis on metabolites. Each day 25 ml was taken out of the system to simulate passage of stool. Additional samples were taken from the lumen of the colon model for analyzing the composition of the microbiota using the I-Chip platform (description later in this material and methods section). These samples were taken at day 0, day 7 and day 14. Short chain fatty acids (SFCA) and branched chain fatty acids (BCFA) analyses The lumen and dialysis samples were analyzed gas-chromatographically on the concentrations of SCFA and BCFA as follows: Samples were centrifuged (12000 rpm, 5 min) and Edoxaban a mixture of formic acid (20%), methanol and 2-ethyl butyric acid (internal standard, 2 mg/mL in methanol) was added to the clear supernatant. According to the method

described by Jouany [21] as described in detail by van Nuenen et al. [22], a 0.5-μL sample was injected on a GC-column (Stabilwax-DA, C646 molecular weight length 15 m, ID 0.53 mm, film thickness 0.1 mm; Varian Chrompack, Bergen op Zoom, The Netherlands) in a Chrompack CP9001 gas chromatograph using an automatic sampler (Chrompack liquid sampler CP9050; Varian Chrompack). Lactate For lactate analysis the samples were centrifuged as described above. In the clear supernatant both L- and D-lactate were determined enzymatically (based on Boehringer, UV-method, Cat. No. 1112821) by a Cobas Mira plus autoanalyzer (Roche, Almere, The Netherlands), as described in detail by van Nuenen et al. [22]. The analysis is based on the conversion of NAD + into NADH. Ammonia For the analysis for the protein-fermentative metabolite ammonia samples were centrifuged as described above and analyzed as described in detail by Van Nuenen et al. [22]. The analysis is based on the conversion of free ammonia with hypochlorite/phenol reagent into blue indophenol.