MicrobiomeNet

Update History

Our MicrobiomeNet manuscript has been accepted by the NAR 2025 Database Issue (10/2024);
Code cleaning and refactoring for improved performance (09/2024);
Added a tutorial to introduce the main features of MicrobiomeNet (08/2024);
Created the MicrobiomeNet User Forum at our OmicsForum and start to add FAQs (08/2024);
Added Metabolism Compatibility map to show a global view of metabolic competition and complementarity indexes relative to any query microbe (08/2024);
Added Neighborhood Map integrating taxonomy and metabolic distances to show the overall similarities among microbes/taxa (07/2024);
Added microbe-phenotype associations based diseases, host genetics, drug metabolism (07/2024);
Improved support for searching microbe by common names (07/2024);
Improved the loading speed of GEM and pathways (07/2024);
Switching to using DuckDB for improved search performance (07/2024);
Added the search summary page (06/2024);
Users can click the node and edges from co-occurrence network to visit the associated GEMs (06/2024);
Updated the layout of the website (06/2024);
Enhances the co-occurrence network visual exploration (06/2024);
Updated the taxonomy information to be consistent with the latest NCBI release (04/2024);
MicrobiomeNet can now compute competition and complementarity indexes for any pair of microbes (01/2024);
Updates the visualization of GEM (10/2023);
Added search and visualization support for microbe-metabolite association network (07/2023);
Added search and visualization support for microbe-microbe co-occurrence network (06/2023);
Added search and visualization support for metabolic pathways based on subsystems (06/2023);
Added searchable data table for microbes and metabolites (05/2023);
Started building the pathway and network libraries for search and visualization (05/2023);
Collected another ~7000 GEMs more and performed data cleaning (05/2023);
Completed curating the taxonomy info for the taxa from the interaction database (04/2023);
A total of ~125,000 microbial associated were curated (02/2023);
Started collecting the microbial association data from literature and public databases (03/2022);
Our TrpNet (https://trpnet.ca) is now published on Metabolites (12/2021);
Developed web-based database, TrpNet, for understanding tryptophan metabolism across gut microbiome (07/2021-12/2021);
Built the microbial tryptophan metabolites library based on the GEM collection (06/2021);
Updated the information from GEM to obtain metabolites, reactions, enzymes and reactions tables (08/2020);
Added the origin information for microbes in the database (08/2020);
About 6000 GEMs were collected and parsed (06/2020);
Started collecting GEMs to support functional analysis for microbiome data (09/2019);