The Lactobacillus sp. indicated by the black arrow, initially present both in the luminal and the mucosal microbial community, were lost during the treatment. On the contrary, the treatment selectively enhanced those species within the dashed square, species that preferentially adhere to the simulated gut surface. These molecular data showed that by means of an HMI module connected to the SHIME, it was possible to evaluate the modulating effect of the test product both on the luminal and mucosa-associated microbiota. The latter was different from the luminal one (in terms of relative abundance of the main species) as the mucin layer is colonized by a biofilm with bacterial species that

specifically (i) adhere to mucins, (ii) metabolize mucins Luminespib chemical structure or (iii) proliferate in mucus due to the microaerophilic conditions at the bottom of this layer. This is also the case in vivo, where it was shown for instance that the mucosa-associated microbiota differs from the dominant fecal microbiota in both healthy subjects and patients with IBD [46]. Figure 5 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; selleck chemicals 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). Parvulin Clustering analysis was based on the Pearson product–moment correlation coefficient and dendrograms were created by using UPGMA linkage. Finally, the positioning of two specific microbial groups (i.e. bifidobacteria and Faecalibacterium prausnitzii) in the mucus layer as analysed by FISH, provided an this website additional proof of the validity of the HMI module as compared to the in vivo situation (Figure 6). While the strict anaerobic bifidobacteria

tended to colonize the upper side of the mucus layer, F. prausnitzii mainly occurred in the lower part of the mucus, i.e. at the anoxic/oxic interphase (Figure 6a). Khan et al. demonstrated that F. prausnitzii can grow in the oxic-anoxic interphase due to the fact that this microorganism, despite being oxygen sensitive, copes with O2 because of a special extracellular electron shuttle of flavins and thiols [47]. Similar to the in vivo situation – where small amounts of oxygen permeate from blood vessels towards the gut lumen – in the HMI module, oxygen diffusion from the aerobic lower chamber to the anaerobic upper chamber (Figure 1) probably results in microaerophilic conditions at the base of the biofilm, allowing for F. prausnitzii to specifically colonize this niche. The qPCR data showed a decreasing concentration of F.