Predicting the Longitudinally and Radially Varying Gut Microbiota Composition using Multi-Scale Microbial Metabolic Modeling
Abstract
:1. Background
2. Results
2.1. A dynamic Framework for Simulating Spatially Differential Gut Microbiota Metabolism
2.2. Overview of the Simulation Results
2.3. Mucosal Microbiota
2.4. Luminal Microbiota
2.5. Inconclusive Firmicutes-to-Bacteroidetes Ratio
2.6. Sensitivity of Parameters
3. Discussion
3.1. A Dynamic Model Capturing the Spatial Distribution of Aerobes vs Anaerobes
3.2. Parameters Regarding Oxygen Availability and Uptake
3.3. Potential Future Extension of the Model
4. Materials and Methods
4.1. Metabolic Models and Nutrient Availability
4.2. Mucosal Microbiota
SI.P | SI.M | SI.D | Cecum | LI.P | LI.M | LI.D | |
---|---|---|---|---|---|---|---|
Default | 6.75 × 10−6 | 2.7 × 10−6 | 1.5 × 10−5 | 1.95 × 10−4 | 5.25 × 10−4 | 7.5 × 10−6 | 9 × 10−6 |
Test 1 | 1 × 10−6 | 1 × 10−6 | 1 × 10−6 | 1 × 10−6 | 1 × 10−6 | 1 × 10−6 | 1 × 10−6 |
Test 2 | 1 × 10−5 | 1 × 10−5 | 1 × 10−5 | 1 × 10−5 | 1 × 10−5 | 1 × 10−5 | 1 × 10−5 |
Test 3 | 1 × 10−4 | 1 × 10−4 | 1 × 10−4 | 1 × 10−4 | 1 × 10−4 | 1 × 10−4 | 1 × 10−4 |
4.3. Luminal Microbiota
4.4. Connecting the Luminal and Mucosal Microbiota
4.5. Oxygen Availability
(mmol h−1g−1) | SI.P | SI.M | SI.D | Cecum | LI.P | LI.M | LI.D |
---|---|---|---|---|---|---|---|
Default | 1.6 × 10−6 | 1.6 × 10−6 | 1.6 × 10−6 | 1.6 × 10−6 | 1.6 × 10−6 | 1.6 × 10−6 | 1.6 × 10−6 |
Test 1 | 0.8 × 10−6 | 0.8 × 10−6 | 0.8 × 10−6 | 0.8 × 10−6 | 0.8 × 10−6 | 0.8 × 10−6 | 0.8 × 10−6 |
Test 2 | 3.2 × 10−6 | 3.2 × 10−6 | 3.2 × 10−6 | 3.2 × 10−6 | 3.2 × 10−6 | 3.2 × 10−6 | 3.2 × 10−6 |
Test 3 | 1.6 × 10−6 | 1.52 × 10−6 | 1.44 × 10−6 | 1.36 × 10−6 | 1.28 × 10−6 | 1.2 × 10−6 | 1.12× 10−6 |
Test 4 | 1.6 × 10−6 | 1.44 × 10−6 | 1.28 × 10−6 | 1.12 × 10−6 | 0.96 × 10−6 | 0.8 × 10−6 | 0.64× 10−6 |
SI.P | SI.M | SI.D | Cecum | LI.P | LI.M | LI.D | |
---|---|---|---|---|---|---|---|
Default | 0.2 | 0.15 | 0.15 | 0.01 | 0.05 | 0.05 | 0 |
Test 1 | 0.4 | 0.3 | 0.3 | 0.05 | 0.1 | 0.1 | 0 |
Test 2 | 0.4 | 0.4 | 0.4 | 0.4 | 0.4 | 0.4 | 0.4 |
Test 3 | 0.2 | 0.2 | 0.2 | 0.2 | 0.2 | 0.2 | 0.2 |
Test 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
(mmol gdw−1h−1) | SI.P | SI.M | SI.D | Cecum | LI.P | LI.M | LI.D |
---|---|---|---|---|---|---|---|
Default | 0.24 | 0.59 | 0.11 | 0.008 | 0.003 | 0.21 | 0.18 |
Test 1 | 2.4 | 2.4 | 2.4 | 2.4 | 2.4 | 2.4 | 2.4 |
Test 2 | 0.24 | 0.24 | 0.24 | 0.24 | 0.24 | 0.24 | 0.24 |
Test 3 | 0.024 | 0.024 | 0.024 | 0.024 | 0.024 | 0.024 | 0.024 |
Test 4 | 0.0024 | 0.0024 | 0.0024 | 0.0024 | 0.0024 | 0.0024 | 0.0024 |
Test 5 | 0.00024 | 0.00024 | 0.00024 | 0.00024 | 0.00024 | 0.00024 | 0.00024 |
4.6. Simulation Parameters
4.7. Availability of Data and Materials
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Chan, S.H.J.; Friedman, E.S.; Wu, G.D.; Maranas, C.D. Predicting the Longitudinally and Radially Varying Gut Microbiota Composition using Multi-Scale Microbial Metabolic Modeling. Processes 2019, 7, 394. https://doi.org/10.3390/pr7070394
Chan SHJ, Friedman ES, Wu GD, Maranas CD. Predicting the Longitudinally and Radially Varying Gut Microbiota Composition using Multi-Scale Microbial Metabolic Modeling. Processes. 2019; 7(7):394. https://doi.org/10.3390/pr7070394
Chicago/Turabian StyleChan, Siu H. J., Elliot S. Friedman, Gary D. Wu, and Costas D. Maranas. 2019. "Predicting the Longitudinally and Radially Varying Gut Microbiota Composition using Multi-Scale Microbial Metabolic Modeling" Processes 7, no. 7: 394. https://doi.org/10.3390/pr7070394