FISH analyses a) positioning of F. prausnitzii (left panel - fluorescent microscopy) and bifidobacteria (right panel - Confocal Laser Scanning Microscopy) in the microbial biofilm with respect to the membrane and mucus layer (M), as indicated by the white arrows. Oxygen concentration (O2) is assumed to decrease from the bottom to the top of the biofilm. The green background is auto-fluorescence of the matrix: EPS, and non-responding bacteria in the left panel, while in the right panel it corresponds to bacteria stained with the EUB338 probe FITC labeled, and also some auto-fluorescent EPS. b) Concentration of F. prausnitzii (F.p.) and Bifidobacterium spp. (Bif.) in the lumen of the SHIME (L) and mucus layer (M) of the HMI module during the treatment period determined by specific qPCR (n = 3).