microbetagDB consists of 34,608 high-quality Genome Taxonomy DataBase genomes, along with their corresponding KEGG annotations and genome-scale metabolic reconstructions.
Seed sets (externally acquired compounds) were retrieved from the latter, supporting the prediction of over 1 billion potential pairwise metabolic interactions.
Relying on KEGG MODULE definitions, 342,000 unique pathway complements were identified based on pairwise overlaps between the annotated genomes.
In addition, 33 phenotypic traits (e.g., pH optima, oxygen tolerance etc.) were predicted for the annotated genomes and incorporated in microbetagDB.
microbetag maps node taxonomies to their closest genome in microbetagDB and annotates them with phenotypic traits and functional potential derived from the literature.
Edges are then annotated with pathway complements and seed complementarities that may represent cross-feeding relationships.
In this repository you may find:
- in the current
developbranch, the precalculation steps/scripts to buildmicrobetagDB - in the
preprocessbranch, the microbetag-preprocessing stand-alone tool, provided as a Docker image - in the
user-binsbranch, a stand-alone version of microbetag to use with custom genomes, instead of mapping taxa to the GTDB representative genomes, provided as a Docker image too
For tutorials on how to use the different parts of the microbetag software ecosystem, please go through our documentation website.
For any issues, feel free to open an issue here on GitHub or contact us on the Matrix microbetag community.
To visualise microbetag-annotated networks but also to perform microbetag for simple cases without any need of running something locally, we provide a
Cytoscape app.
The source code for the microbetag GUI can be found here.
This project is funded by an EMBO Short-Term Fellowship and the 3D’omics Horizon project (101000309).