MicrobiomeNet is a comprehensive database that brings together known statistical associations and genome-scale metabolic models (GEMs) to facilitate hypothesis generation and mechanistic insights. GEMs depict organisms' nutritional requirements which can be used to infer their potential metabolic interactions for their observed co-occurrence patterns. A three-step strategy was implemented:

1. Starting with a microbe of interest, search for its known co-occurrence patterns according to study contexts, taxonomic resolutions, statistical methods, etc → Association Table & Network.
2. From these statistically associated microbes, investigate their metabolic & taxonomic distances, metabolic competition & complementarity profiles → Neighbourhood Map & Metabolism Compatibility Map.
3. From the most promising candidates, examine their underlying metabolic dependencies → GEM & Pathway Network Visual Analytics.

Microbial Association Networks

MicrobiomeNet currently contains ~ 6 million microbial statistical associations detected using different algorithms including Spearman, Pearson, SparCC, FlashWeave, MINE, Dice Index, and Binding. They have been collected from 76 studies covering diverse environments. Users can intuitively search and visually explore these networks.

Genome-Scale Metabolic Models (GEMs)

GEMs contain all known metabolic information including the genes, enzymes, reactions, and metabolites of a biological system. They are powerful tools to predict cellular metabolism and physiological states in living organisms. MicrobiomeNet currently contains 12,400 GEMs covering a broad ranges of taxonomies. Users can search, view and compare GEMs for microbes of interest.

Pathways and Subsystems

Pathways (also known as subsystems) are a set of reactions that share a similar metabolic function. MicrobiomeNet currently contains a total of 137 pathways extracted from the GEMs. Mouse over any colored shape to view a detailed summary of the corresponding pathway. Click to explore the pathway.