Table 2 Bacterial concentration of different

microbial groups quantified by specific qPCR in ATM inhibitor luminal (L) (n = 3) and mucosal (M) (n = 6) samples of the HMI module during control and treatment at time 0, 24 and 48 h     Control (A) Treatment (B)     0 h 24 h 48 h 0 h 24 h 48 h     L L M L M L L M L M Total Bacteria Avg. 2.46 × 1010 1.31 × 1010 5.71 × 108 9.08 × 109 6.35 × TGF-beta inhibitor 108 6.35 × 10 9 6.27 × 10 9 2.43 × 10 8 7.79 × 109 2.31 × 10 7   Std. 1.12 × 109 1.53 × 108 2.83 × 108 4.77 × 108 8.44 × 108 3.14 × 108 7.54 × 107 1.75 × 108 2.29 × 108 2.56 × 106 Bacteroidetes Avg. 7.60 × 109 6.29 × 109 5.25 × 108 4.58 × 109 2.78 × 108 1.41 × 10 9 4.50 × 109 9.82 × 10 7 1.13 × 10 10 6.59 × 107   Std. Dev. 1.23 × 109 2.77 × 109 3.60 × 108 1.20 × 109 3.65 × 108 1.83 × 108 6.96 × 108 6.07 × 107 1.79 × 109 3.44 × 107 Firmicutes Avg. 1.65 × 109 1.64 × 108 2.08 × 107 2.85 × 108 1.67 × 107 7.88 × 10 8 4.29 × 10 8 3.65 × 106 5.43 × 10 8 9.65 × 10 5   Std. Dev. 2.79 × 108 1.02 × 107 3.80 × 106 2.52 × 107 3.20 × 106 7.21 × 107 3.96 × 107 1.60 × 106 4.11 × 107 7.41 × 105 Bifidobacteria Avg. 9.39 × 108 2.73 × 108 3.35 × 108 3.24 × 108 8.49 × 106 1.26 × 10 8 3.79 × 108 1.25 × 10 6 4.43 × 10 8 3.37 × 10 5   Std. Dev. 1.23

× 108 2.65 × 107 5.09 × 107 2.97 × 107 9.80 × 105 2.89 × 107 1.40 × 108 1.38 × 105 2.44 × 107 1.74 × 105 Lactobacilli Avg. 1.88 × 107 3.86 × 106 1.30 × selleck screening library 105 6.81 × 105 3.45 × 102 8.06 × 10 5 3-oxoacyl-(acyl-carrier-protein) reductase 1.77 × 10 5 1.45 × 10 3 1.37 × 106 5.85 × 10 4   Std. Dev. 3.47 × 106 3.45 × 105 7.75 × 104 5.40 × 105 3.89 × 102 1.69 × 105 1.54 × 105 1.67 × 103 2.52 × 105 7.86 × 104 Data for L are expressed as 16S rRNA gene copies/mL of SHIME suspension; those for M correspond to 16S rRNA gene copies cm−2 of simulated gut wall. Values in bold indicate samples from the treatment period which are significantly higher than the control at the same sampling time, according to a Student’s two-tailed t test (p < 0.05). Values in italics are significantly lower. The

cluster analysis based on a composite data set of the DGGE gels for total bacteria (Additional file 1: Figure S2), bifidobacteria (Figure 5a) and lactobacilli (Figure 5b) is shown in Figure 5c. The samples from control and treatment period clustered separately (cluster I and II). Moreover, within each cluster, luminal samples and mucosal samples sub-clustered in two different groups (Figure 5c).