MicrobiomeNet is a comprehensive database and visualization platform aiming to integrate microbial associations with their metabolic profiles for mechanistic insights.
MicrobiomeNet contains >12,000 genome-scale metabolic models (GEMs), ~5.8M microbe-microbe associations and ~30K phenotype-microbe associations as the backend database. It allows intuitively mining of known microbial associations (i.e. co-occurrences patterns) within the context of their metabolite profiles (i.e. GEMs) for mechanistic insights. The underlying assumption is that the direct metabolic interactions are rare among their known statistical associations. Focusing on a query microbe, MicrobiomeNet provide the a three-step sequential strategy to identify the potential metabolic interaction among the reported statistical associations :
- Starting from a given microbe, search and identify its known co-occurrence patterns according to study contexts, taxonomic resolutions, statistical methods, etc → Association Table & Network .
- From these associated microbes, investigate their metabolic & taxonomic distances, metabolic competition & complementarity profiles → Neighbourhood Map & Metabolism Compatibility Map.
- From the most promising microbes, pinpoint their underlying metabolic dependencies → GEM & Pathway Network Visual Analytics.
You can also start from metabolites, enzymes, SNPs, phenotypes, drugs to find known associated microbes and then follow the above process.