Fig 1.
Model for construction of a synthetic community.
A joint model for pairwise communities unites all species’ GEM into one, with an extracellular environment for exchanging metabolites between the species.
Fig 2.
The joint metabolic network model of two toy models.
Metabolites are represented with circles. Since all reactions in the toy model are reversible, we separate each reaction into two irreversible reactions.
Fig 3.
The pseudocode and a graphical representation of the CPARMA algorithm outcome.
(a) Organism 1 can supply shared metabolites while its growth remains unaffected: This is known as commensalism interaction. (b) Species 2 is parasitic to species 1, and this relationship is termed parasitism. (c) Species 2 cannot survive in the absence of species 1 with just the concentration from the environment (d) Species 2 can survive by utilizing the supplied metabolites from both the environment and species 1.
Table 1.
Comparison of the COMMA and CPARMA methods with other interaction prediction tools using metabolic models.
Fig 4.
Predicted competed and overlapping metabolites of pairwise interactions between seven microbial species.
(a) The number of overlapped metabolites. (b) The competition rate. Each color of the chord in the diagram is unique to one of the 21 pairs of species. The degree of color and widths of the chords increases from alice blue to dark blue as the competition rate and overlapped metabolites increase.
Table 2.
Our algorithm competition score and dissimilarity metrics of phyllosphere-asscoiated strains in relation to Pe299R.
Fig 5.
Population density of Pe299R over time.
The population size of Pe299R, in the presence of other strains, changes at different times. The total population density increased over time in a similar pattern as the population density in the monoculture also increased.