Metabolism Compatibility Map, display as a scatter plot, integrates complementarity index (x-axis) and competition index (y-axis) for all taxa covered in MicrobiomeNet based on GEMs.
Seed metabolite:
The minimal group of external compounds required by a specific organism to
produce all other compounds in its metabolism.
Competition index:
The similarity of the nutrition requirement of two microbes, denoted by the proportion
of shared seed metabolites.
Complementarity index:
The potential for one microbe to produce the seed motabolite required by another
microbe.
The image below illustrates the overall concepts (original paper)
Would you be able to explain a little further as to what the interpretation is for the positive and negative associations? I know that it is based on the association weight from the individual reference provided, but I am unsure on how to further understand what it means biologically.
The positive/negative associations are statistical associations we curated from literature/ references. They are also known as “co-occurrence patterns” - i.e. two microbes tend to show up together more often than expected by random (positive association), or never show up together (negative association). You can read the specific algorithms used to compute these values (i.e. what are the null models used to estimated the random chance).
MicrobiomeNet is designed to help detect biologically interpretable co-occurrence patterns based on the metabolic capacities defined by their GEMs
