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Metabolic modeling tutorial for EMBO practical course: Metabolite and species dynamics in microbial communities 2022

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🔬 EMBOMicroCom: Metabolite and species dynamics in microbial communities 🧬

DOI

💻 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

  1. Start by cloning this repo
  2. Inspect metabolic models and media file
  3. Simulate community interactions between bacteria and yeast
  4. Explore effect of interactions as a function of media composition
  5. 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