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embomicrocom

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

https://github.com/franciscozorrilla/embomicrocom

Science Score: 64.0%

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Keywords

flux-balance-analysis genome-scale-metabolic-model microbial-ecology
Last synced: 6 months ago · JSON representation ·

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

Basic Info
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  • Stars: 13
  • Watchers: 1
  • Forks: 2
  • Open Issues: 1
  • Releases: 1
Topics
flux-balance-analysis genome-scale-metabolic-model microbial-ecology
Created over 3 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Citation

README.md

🔬 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

Owner

  • Name: Francisco Zorrilla
  • Login: franciscozorrilla
  • Kind: user
  • Location: Cambridge, UK
  • Company: MRC Toxicology, University of Cambridge

PhD Student in the Patil Lab. Interested in metagenomics, metabolic modeling of microbial communities, and machine learning

Citation (CITATION.bib) 

@software{francisco_zorrilla_2022_7414248,
  author       = {Francisco Zorrilla},
  title        = {franciscozorrilla/EMBOMicroCom: Materials},
  month        = dec,
  year         = 2022,
  publisher    = {Zenodo},
  version      = {v1.0.0},
  doi          = {10.5281/zenodo.7414248},
  url          = {https://doi.org/10.5281/zenodo.7414248}
}

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