Supplementary Figure 2 (A) Schematic representation of the third experiment in which two colon units with a simulated mucosal environment containing mucins.

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Supplementary Figure 2 (A) Schematic representation of the third experiment in which two colon units with a simulated mucosal environment containing mucins (M(+)-SHIME), two colon units with a simulated mucosal environment free of mucins (M(-)-SHIME) and two colon units without mucosal environment (L-SHIME) were inoculated with two different human faecal samples (donor A or D). (B) Dendrogram for the total bacterial DGGE profiles of the luminal and, if applicable, mucosal samples of the two M(+)-SHIMEs, two M(-)-SHIMEs and two L-SHIMEs, three days after inoculation with faecal samples of two human subjects (A and D). The average inter-individual similarity between different donors (± SEM) is shown for each type of sample: inoculum, lumen, mucin (-)and mucin (+) layer.