A comprehensive framework for reconstructing and analyzing community genome-scale metabolic models (cGEMs) from metagenomic data.

🎯 Overview

cGEM-FORGE is a complete pipeline for building, analyzing, and visualizing community genome-scale metabolic models (cGEMs) from metagenomic data. The framework integrates several tools into a streamlined workflow for studying microbial community metabolism.

🔧 Features

• Automated reconstruction of individual genome-scale metabolic models (GEMs) from MAGs using CarveMe
• Community model building using MICOM
• Analysis of metabolic exchanges and trophic interactions
• Multiple visualization options for metabolic interactions
• Docker containers for easy deployment and reproducibility

📋 Requirements

• Docker
• Input files:
  • MAGs (Metagenome-Assembled Genomes) as protein FASTA files
  • Relative abundance data (TSV format)
  • Medium composition file (TSV format)
  • Universal model file (XML format)

🚀 Pipeline Steps

1. Individual GEM Reconstruction

   • Uses CarveMe to build metabolic models for each MAG
   • Outputs individual models in XML format

2. Medium Preparation

   • Generates MICOM-compatible medium files from media database
   • Configurable medium composition and uptake rates

3. Community Model Construction

   • Creates MICOM taxonomy table
   • Builds integrated community model
   • Outputs pickled community model

4. Exchange Analysis

   • Computes metabolic exchanges between community members
   • Analyzes trophic interactions
   • Configurable growth trade-offs

5. Visualization

   • Network diagrams of trophic interactions
   • Heatmaps of metabolic exchanges
   • Sankey diagrams of metabolic flows

💻 Usage

The framework consists of several Docker containers that can be run sequentially:

1. CarveMe Container

docker run \
  -v /path/to/microcom:/app/microcom \
  -v /path/to/config.tsv:/app/config.tsv \
  -v /path/to/results:/app/results \
  ghcr.io/new-atlantis-labs/carveme:latest \
  --config /app/config.tsv \
  --outdir /app/results \
  --processes 10

2. MICOM Container

docker run \
  -v /path/to/data:/app/data \
  -v /path/to/results:/app/results \
  ghcr.io/new-atlantis-labs/micom:latest \
  build_cgem \
  --taxa_table /app/data/micom_database.tsv \
  --outdir /app/results \
  --abundance_cutoff 0.01 \
  --threads 10 \
  --solver "hybrid"

3. Visualization Container

docker run \
  -v /path/to/data:/data \
  -v /path/to/results:/app/results \
  ghcr.io/new-atlantis-labs/cgem-viz:latest \
  --exchanges-file /data/exchanges.tsv \
  --visualization-type network

📊 Visualization Options

The framework supports three types of visualizations:

1. Network Diagrams

   • Shows trophic interactions between community members
   • Configurable flux cutoffs
   • Directed edges indicating metabolite exchanges

2. Exchange Heatmaps

   • Visualizes metabolic exchanges between species
   • Optional normalization and clustering
   • Customizable color schemes

3. Sankey Diagrams

   • Displays metabolic flows in the community
   • Configurable flux cutoffs
   • Interactive visualization of metabolite transfers

📝 Input File Formats

1. Abundance File (TSV)

id    taxonomy    abundance
MAG1  Species1    30
MAG2  Species2    40

2. Medium Composition (TSV)

reaction_id    max_uptake
EX_glc_e      10.0
EX_o2_e       5.0

🤝 Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

📄 License

This project is licensed under the MIT License - see the LICENSE file for details.