Table 1 Description of the metrics used. Here, the term “community” means either the whole community or a random subsample of strains (SynCom). The acronyms in bold in the table are used throughout the text

Nutritional constraint

Available nutrients on which a GEM can rely on (i.e., the initial reactants of the whole network). Nutritional constraints are modeled with simulated growth media. In this paper, an “unconstrained” GEM represents its metabolic potential, i.e., all the metabolites it encodes and can theoretically produce.

Predicted Producible Metabolites (PPM)

The list (number and composition) of all metabolites predicted to be producible by one or several GEMs simultaneously (also referred to as a meta-GEM), under a nutritional constraint or in the absence of a constraint. This metric is used to summarize the unconstrained and constrained (by available nutrients) metabolism inferred from genomes.

Core Predicted Producible Metabolites (CPPM)

The part (number and composition) of a community PPM which is individually producible by each GEM individually in a set of GEMs.

Targeted Predicted Producible Metabolites (TPPM)

A set of 30 metabolites on which part of this study is focused. Their ability to be produced by one or several GEMs is analyzed (number and composition), under a nutritional constraint or in the absence of a constraint.

Community added value

The part of the PPM (number and composition) of several GEMs which is only producible by metabolic interactions within a community (i.e., not producible by a single GEM).

Average phylogenetic distance

The average of all pairwise phylogenetic distances between pairs of strains in a synthetic subsample of strains (SynCom). The whole community also has an average phylogenetic distance.