FIGURE LEGENDS
FIGURE 1 Schematic representation of a bioreactor module.
FIGURE 2 Aerobic and anaerobic growth of a gut bacteria. (A) Growth of Bifidobacterium longum subspecies infantis (B. infantis) monocultures under anaerobic conditions at pH 5.8. Data shown is the average of two trials with n=4 replicates. (B) Abundance of bacteria detected by the bacterial 16S rDNA universal primers and 16S rDNA primers specific for Bifidobacterium longum in equivalent masses of input template DNA extracted from the monocultures in (A). Data shown is the average of two trials with n=4 replicates. (C) Growth of a model gut microbiota (mixed bacterial cultures) over time in aerobic and anaerobic conditions maintained at pH 5.8. Data shown is the average of two trials with n=2 replicates. (D) Proportions of bacterial genera present in the starter culture (0 h) and after 24 h of growth in aerobic and anaerobic cultures (C). *P < 0.05.
FIGURE 3 Growth of a bacterial monocultures with and without pH control. Growth of an E. coli monocultures over time (A) without pH control and (B) at pH 7.0. (C) Total volume of acid and base added to the pH-controlled culture (B) over time. Data shown is the average of 2 trials with n=3 replicates.
FIGURE 4 Stability of the genotype of a model gut microbiota in a dynamic simulation of the human digestive tract. (A) The pH setpoint of the culture medium representing segments of the simulated digestive tract. The rate of influx and efflux of culture medium into and out of each bioreactor was set to 0.1 mL/min. (B) Proportions of bacterial genera of the starter culture. The growth of the model gut microbiota over 5 days and the proportions of bacterial genera assayed at 24, 72, 120 h in modules representing (C) Stomach (Module 1), (D) Proximal small intestine (Module 2), (E) Distal small intestine (Module 3), (F) Ascending colon (Module 4), (G) Transverse colon (Module 5) and (H) Descending colon (Module 6). The areas of the circles depict the density of the bacterial cultures at the time of sampling with the density of the inoculum (B) set to 100 %. Data shown is the average of 2 trials with n=2 replicates.
FIGURE 5 Functionality of a model gut microbiota in response to bile acid treatment. (A) Growth of a model gut microbiota in the anaerobic conditions at pH 5.8 in the absence or presence of taurocholic acid (TCA). Data shown is the average of two trials with n=2 replicates. (B) Proportions of bacterial genera present at inoculation (0 h) and after 24 h of culture (A). (C) Representative chromatogram showing the detection of TCA and cholic acid (CA) in the growth medium of inoculated cultures at 0 h and 24 h, and uninoculated culture (no bacteria) at 24 h, in the presence of 10 mM TCA. (D) Growth of a model gut microbiota in the presence of chenodeoxycholic acid (CDCA). Data shown is the mean of 2 trials with n=4 replicates. (E) Detection of CDCA and ursodeoxycholic acid (UDCA) in the growth medium at inoculation (0 h) and after 24 h of culture. ND, not detected.
FIGURE S1 Algorithm of the bioreactor control software.
FIGURE S2 Example configurations of simulated gut models.
FIGURE S3 Species composition of the bacterial community present in specific bioreactor modules of the dynamic simulation of the human digestive tract as described in the legend of FIGURE 4.