Metabolic modeling tutorial for EMBO practical course: Metabolite and species dynamics in microbial communities
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🔬 EMBOMicroCom: Metabolite and species dynamics in microbial communities 🧬
![DOI](https://zenodo.org/badge/550822801.svg)
💻 Metabolic modeling tutorial (Day 5)
💰 Learning Outcomes
- Predict metabolic interactions within microbial communities
- Explore the effect of media composition on the predicted metabolite exchanges
- Interpret predicted metabolic interactions and evaluate against experimental data
📚Suggested Reading
- Case study: Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow
- Intro to FBA: What is flux balance analysis?
- SMETANA: Metabolic dependencies drive species co-occurrence in diverse microbial communities
- CarveMe: Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
⛏ Materials
models/bacteria.xml
: Manually refined Lactococcus lactis genome scale metabolic model
models/yeast.xml
: Manually refined Saccharomyces cerevisiae genome scale metabolic model
media.tsv
: Media composition file used for simulation under differing environments
bigg_classes.tsv
: BiGG metabolite ID dictionary and metadata
plot_interactions.R
: Rscript for generating alluvial diagrams based on SMETANA output
🎯 Exercises
- Start by cloning this repo
- Inspect metabolic models and media file
- Simulate community interactions between bacteria and yeast
- Explore effect of interactions as a function of media composition
- Generate metabolic models and predict interactions using your own genomes (BONUS)
🏄 Metabolic Modeling Repos
Resources
Tools
- metaGEM: Reconstruction and simulation of genome scale metabolic models directly from metagenomes
- DesignMC: Design microbial communities for production of specific target compounds using GEMs
- HiOrCo: Compute higher order cooccurence using abundance across samples
- Reframed: Metabolic modeling package
🥼 Contributors
- Francisco Zorrilla, MRC Toxicology Unit - University of Cambridge
- Kiran R. Patil, MRC Toxicology Unit - University of Cambridge