mmnet

mmnet reconstructs and analyzes community-level metabolic networks from metagenomic reads as an R package by mapping functional annotations to KEGG global metabolic pathways to characterize microbial community metabolic capabilities.

Key Features:

• Metagenomic systems biology mapping to KEGG: Maps metagenomic data onto KEGG global metabolic pathways to enable systems-level network construction.
• Automated analysis pipeline: Provides functions for functional annotation of metagenomic reads, enzymatic gene abundance estimation, and community-level metabolic network reconstruction.
• Integrated network analysis: Performs topological and functional analyses of reconstructed networks to explore regulation and metabolic functionality within metagenomes.
• Network export: Exports reconstructed networks for downstream visualization in Cytoscape.

Scientific Applications:

• Human microbiome disease association: Identifies system-level variations in community metabolic networks associated with health and disease in metagenomic studies.
• Functional characterization of microbial communities: Investigates how microbial interactions and enzymatic gene abundances influence community metabolic capabilities and physiological states.

Methodology:

Functional annotation of metagenomic reads; mapping annotated functions to KEGG global metabolic pathways; estimation of enzymatic gene abundances; reconstruction of community-level metabolic networks; and topological analysis of reconstructed networks.