Metage2Metabo

Metage2Metabo reconstructs and analyzes genome-scale metabolic networks from annotated genomes to characterize metabolic functions and metabolic cooperation in large-scale microbiotas.

Key Features:

• Implementation: Implemented in Python 3 (version 3.6 or higher).
• Graph-based metabolic analysis: Employs a graph-based approach for metabolic network reconstruction and analysis of individual and community-level functions.
• Genome-scale reconstruction with Pathway Tools: Reconstructs genome-scale metabolic networks using Pathway Tools and can accept user-provided networks.
• Scalability and parallelization: Uses a multi-processing solution to enable parallel execution of Pathway Tools for handling large numbers of genomes.
• Analysis of individual and collective metabolism: Analyzes networks both individually and collectively to capture functional contributions of organisms.
• Identification of keystone and symbiont species: Identifies keystone species, alternative and essential symbionts by reducing large microbiotas to minimal communities with equivalent properties.
• Application to large datasets: Applied to datasets including 1,520 genomes from gut microbiota and 913 metagenome-assembled genomes (MAGs) from rumen microbiota.

Scientific Applications:

• Functional profiling of microbiotas: Captures functional diversity across large microbiota collections by screening many metabolic networks.
• Keystone species discovery: Identifies organisms critical for community function and potential alternative or essential symbionts.
• Large-scale comparative analysis: Enables comparative evaluation of metabolic capabilities across gut and rumen microbiota datasets.
• Metabolic cooperation analysis: Provides insights into how individual metabolic functions contribute to overall community metabolism.

Methodology:

Reconstruction of genome-scale metabolic networks from annotated genomes using Pathway Tools or user-provided networks; graph-based reconstruction and analysis of networks; multi-processing parallel execution of Pathway Tools for scalability; analysis of networks individually and collectively and reduction to minimal communities to identify keystone, alternative, and essential symbionts.