Table 3 Summary of selected mathematical models for the colonic environment
From: Examination of hydrogen cross-feeders using a colonic microbiota model
Publication (model name) | No. of MFGs | No. of metabolites | Key features |
|---|---|---|---|
Muñoz-Tamayo et al. [31] | 4 | 13 | Lumen, mucous and gaseous compartments over three colonic sections |
Motelica-Wagenaar et al. [2] | 10 | 24 | Proximal colon only, adaptation of Muñoz-Tamayo et al. [31] Parameterised from in vitro data Impact of transit time, substrates, pH, and presence of methanogens investigated |
Moorthy et al. [52] | 4 (multiple strains within MFG) | 10 | One-dimensional spatially continuous adaptation of Muñoz-Tamayo et al. [31] Only carbohydrate substrates considered No gaseous phase Varied transit times, fibre intakes and number of strains in the primary degrader MFG investigated |
Bauer et al. [3] (BacArena) | 7 | 50 +  | Two-dimensional cellular automaton constraint-based reconstruction and analysis (COBRA) model Includes cellular motility and mucin layer |
Van Hoek and Merks [49] | Single supra-organism used | 50 +  | Two-dimensional cellular automaton COBRA model Evolutionary component of metabolic pathway gain/loss No specific MFGs, theoretical organisms with widely varied metabolic capabilities Varied transit times investigated |
Cremer et al. [51] | 2 | 7 | One-dimensional mechanistic model Includes relationship between SCFA production, pH and microbial growth Models water absorption and peristaltic movement of the colon wall |
Labarthe et al. [53] | 4 | 12 | A unification of Muñoz-Tamayo et al. [31] with Cremer et al. [51], also including microbial active motion Diet, mucous, chemotaxis and peristalsis variations investigated |
microPop:Colon | 11 | 20 | Spatially discrete or continuous versions Responsive pH Host secretion and absorption Inclusion of mucins, but no mucous layer or gaseous phase Inclusion of SRB |