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.