DGGE fingerprinting analysis for bifidobacteria (a) lactobacilli (b) and composite data set of the gels for bifidobacteria. lactobacilli and total bacteria, including bootstrap analysis with 1000 samplings (c). A = control period (Cluster II); B = treatment period (Cluster I). L = luminal samples collected from the SHIME reactor; M = mucus sample collected from a fraction of the membrane inside the HMI module. 0, 24 and 48 indicate the hours that the HMI modules have been connected to the SHIME system during the control and treatment periods (as illustrated in Figure 3). Clustering analysis was based on the Pearson product–moment correlation coefficient and dendrograms were created by using UPGMA linkage.