metaGEM from MAGs to predicting metabolic interactions in microbial communities with metabolic modelling

Trainer: Maria Zimmermann, Eva Geissen, Francisco Zorrilla

Overview: This session will focus on hands-on training using metaGEM to predict metabolic interactions.

Learning outcomes

By the end of this session you will be able to:

  • Generate genome-scale metabolic models (GEMs) from metagenome assembled genomes (MAGs)
  • Predict metabolic interactions within bacterial communities
  • Characterize communities using competition-cooperation plot
  • Explore uncertainty in GEM reconstruction and simulation
  • Pros and cons of using reference genomes vs metagenome-assembled or single-amplified genomes for metabolic modeling

Materials:

  • Introduction to hands-on training

Questions for further discussion:

  1. What assumptions are made in genome-scale modelling approach
  2. What input data is required?
  3. What type of data can be integrated, how, and what for? E.g. transcriptomics, proteomics, metabolomics
  4. How would you test the model predictions experimentally?
  5. Can the model predict unexpected interactions?
  6. Do you think this approach could be used in your project?