Processes 2019, 7,97
2.5. Host-Derived Nitrate Perturbations
The human host is known to secrete nitrate in response to inflammation in the gut [17]. Preliminary
FBA calculations showed that nitrate uptake increased the E. coli growth rate, while the other three
community members were unable to use nitrate as an electron acceptor. Therefore, we hypothesized
that host-derived nitrate would increase E. coli abundance during simulated C. difficile-associated
dysbiosis and yield better agreement with experimental studies [71,73]. To quantify the effects of
nitrate availability, biofilm simulations were performed with and without nitrate for a dysbiosis case
with reduced glucose, increased amino acids, and available taurocholate (Table 1).
As hypothesized, the main impact of host-derived nitrate was to substantially increase E. coli
abundance from 4% without nitrate to 20% with nitrate (Figure 5A). The F. prausnitzii abundance
decreased from 7% to 2%, while the abundances of B. thetaiotaomicron and C. difficile decreased modestly
to accommodate the increased E. coli. The species abundances predicted with nitrate are in good
agreement with experimental studies for C. difficile-associated dysbiosis showing large increases in
C. difficile and E. coli, large decreases in F. prausnitzii, and modest changes in B. thetaiotaomicron [85–87].
Figure 5. Predicted multispecies biofilm dysbiosis with and without host-derived nitrate. (A) Biomass
concentrations (bar graphs) and species abundances (pie charts) averaged across the biofilm for the
healthy and dysbiosis case. (B) Acetate, butyrate, propionate, and total SCFA concentrations (mmol/L)
averaged across the biofilm. (C) Succinate, formate, and total OA concentrations averaged across
the biofilm.
Nitrate availability was predicted to increase the acetate and total SCFA concentrations
substantially due to large changes in E. coli and F. prausnitzii abundances (Figure 5B). Decreased
succinate consumption by F. prausnitzii and increased formate synthesis by E. coli results in increased
levels of individual and total OAs (Figure 5C). These predictions implicate a role for host-derived
nitrate in C. difficile-associated dysbiosis.
We investigated the robustness of the four-species community during dysbiosis with available
nitrate by removing selected cross-feeding relationships and varying the biofilm thickness from the
nominal value of 40 microns. When C. difficile uptake of formate or succinate was eliminated, the
C. difficile abundance dropped substantially (Figure S4), further suggesting that these cross-feeding
relationships could be important for C. difficile propagation in vivo. Consistent with our previous
study [50], cross-feeding of ethanol was important for B. thetaiotaomicron growth, and cross-feeding
of both acetate and succinate was necessary for F. prausnitzii co-existence. For biofilm thicknesses of
30–60 microns, the species abundances were predicted to vary substantially with the most important
trend being that thinner biofilms enhanced C. difficile growth (Figures S5 and S6). The growth rate
28
2.5. Host-Derived Nitrate Perturbations
The human host is known to secrete nitrate in response to inflammation in the gut [17]. Preliminary
FBA calculations showed that nitrate uptake increased the E. coli growth rate, while the other three
community members were unable to use nitrate as an electron acceptor. Therefore, we hypothesized
that host-derived nitrate would increase E. coli abundance during simulated C. difficile-associated
dysbiosis and yield better agreement with experimental studies [71,73]. To quantify the effects of
nitrate availability, biofilm simulations were performed with and without nitrate for a dysbiosis case
with reduced glucose, increased amino acids, and available taurocholate (Table 1).
As hypothesized, the main impact of host-derived nitrate was to substantially increase E. coli
abundance from 4% without nitrate to 20% with nitrate (Figure 5A). The F. prausnitzii abundance
decreased from 7% to 2%, while the abundances of B. thetaiotaomicron and C. difficile decreased modestly
to accommodate the increased E. coli. The species abundances predicted with nitrate are in good
agreement with experimental studies for C. difficile-associated dysbiosis showing large increases in
C. difficile and E. coli, large decreases in F. prausnitzii, and modest changes in B. thetaiotaomicron [85–87].
Figure 5. Predicted multispecies biofilm dysbiosis with and without host-derived nitrate. (A) Biomass
concentrations (bar graphs) and species abundances (pie charts) averaged across the biofilm for the
healthy and dysbiosis case. (B) Acetate, butyrate, propionate, and total SCFA concentrations (mmol/L)
averaged across the biofilm. (C) Succinate, formate, and total OA concentrations averaged across
the biofilm.
Nitrate availability was predicted to increase the acetate and total SCFA concentrations
substantially due to large changes in E. coli and F. prausnitzii abundances (Figure 5B). Decreased
succinate consumption by F. prausnitzii and increased formate synthesis by E. coli results in increased
levels of individual and total OAs (Figure 5C). These predictions implicate a role for host-derived
nitrate in C. difficile-associated dysbiosis.
We investigated the robustness of the four-species community during dysbiosis with available
nitrate by removing selected cross-feeding relationships and varying the biofilm thickness from the
nominal value of 40 microns. When C. difficile uptake of formate or succinate was eliminated, the
C. difficile abundance dropped substantially (Figure S4), further suggesting that these cross-feeding
relationships could be important for C. difficile propagation in vivo. Consistent with our previous
study [50], cross-feeding of ethanol was important for B. thetaiotaomicron growth, and cross-feeding
of both acetate and succinate was necessary for F. prausnitzii co-existence. For biofilm thicknesses of
30–60 microns, the species abundances were predicted to vary substantially with the most important
trend being that thinner biofilms enhanced C. difficile growth (Figures S5 and S6). The growth rate
28