NetCom

NetCom predicts metabolic activities in microbial communities by using a network-based interpretation of assembled and annotated metagenomic data to link differential enzymatic reaction abundance with pathways, environmental resources, and compound production to elucidate environment–community–function relationships.

Key Features:

• Input Requirements: Accepts lists of differentially abundant enzymatic reactions derived from metagenomic data as the primary input.
• Pathway Associations: Identifies and associates metabolic pathways with enzymes that show differential abundance across conditions.
• Environmental Resource Prediction: Predicts unique environmental resources for each treatment condition and links them to specific metabolic pathways.
• Compound Production Prediction: Forecasts compounds produced by the microbial community and delineates pathway associations for treatment-specific compounds.
• Network Visualization: Produces 2D and 3D network representations including enzymes, environmental resources, and produced compounds, highlighting elements unique to specific treatments.

Scientific Applications:

• Ecological and environmental microbiology: Supports studies that infer community-level metabolic activities from metagenomic enzyme abundance data.
• Rhizosphere and root-specific activity prediction: Predicts root-specific activities and forecasts how soil amendments may impact microbial community functions in rhizospheres.
• Nutrient cycling: Aids investigation of ecosystem functions such as nutrient cycling by linking enzymes and pathways to environmental resources and compounds.
• Plant–microbe interactions: Enables analysis of metabolic processes relevant to plant–microbe interactions through pathway and compound predictions.

Methodology:

Implements a network-based approach that integrates differential abundance information of enzymatic reactions from assembled and annotated metagenomic data to construct metabolic networks linking enzymes, pathways, environmental resources, and produced compounds.