This package includes an example directory containing models and media specifications, enabling users to perform a straightforward analysis using misosoup. The example demonstrates how to identify minimal microbial communities that utilize acetate as the sole carbon source. The results of this analysis are pre-generated and available in the directory for reference.

Running the Example

To execute the analysis, navigate to the example directory and use the following command:

cd example/marine/
misosoup ./strains/*.xml --output ./output.yaml --media media.yaml --strain A1R12 --media-select ac

This command instructs misosoup to analyze the specified microbial strains for their ability to support the growth of strain A1R12 in a Minimal Basal Medium (MBM) with acetate (ac) as the exclusive carbon source.

Analysis Results

The simulation results, detailed in output.yaml, reveal two potential microbial communities capable of supporting A1R12 growth:

  • Solution 1: Community comprising A1R12 and I2R16, indicating a symbiotic relationship sufficient for growth on acetate.
  • Solution 2: Community comprising A1R12 and I3M07. Detailed analysis of this community shows:
    • Both strains produce carbon dioxide as a by-product, with strain-specific CO2 fluxes of R_EX_co2_e_A1R12_i: 0.564 for A1R12 and R_EX_co2_e_I3M07_i: 0.1312 for I3M07.
    • The total community-level carbon dioxide production is quantified by the flux R_EX_co2_e: 1.695, highlighting the combined metabolic activity.

These solutions showcase misosoup’s ability to predict minimal microbial communities based on specific metabolic requirements, facilitating targeted research and application in microbial ecology and synthetic biology.