Table 1 Overview of the interaction prediction tools and their parameters
From: Predicting microbial interactions with approaches based on flux balance analysis: an evaluation
Tool | Input | Community approach | Optimisation aproach | Community biomass function | Output | Special capabilities | Method ID | Tool parameters |
|---|---|---|---|---|---|---|---|---|
COMETS | List of GEMs along with their corresponding initial biomass for each community | Dynamic | Maximizes each species biomass sequentially considering their initial biomass and total uptake then updates species' biomass and extracellular compound concentrations | No | Growth curves =  > Growth rates and maximal biomass | Spatial dimension Time dimension Chemostat or batch | H | param = test_tube timeStep = 1 maxCycles = 10 initial_pop = 1 g/sp objective_style = MAXIMISE_OBJECTIVE_FLUX and MAX_OBJECTIVE_MIN_TOTAL |
H/10 | param = test_tube timestep = 0.1 maxCycles = 20 initial_pop = 0.002 g/sp objective_style = MAXIMISE_OBJECTIVE_FLUX and MAX_OBJECTIVE_MIN_TOTAL | |||||||
MICOM | List of GEMs from each community (samples) | Cooperative trade-off | Maximizes community growth rate (sum of the individual growth rates) then, limits community growth to only a fraction of its maximum rate to create a trade-off between optimal community growth and individual growth rate maximization | Yes | Growth rates | Like OptCom but in a more efficient, simpler implementation. Growth rate estimates dependent on species abundance in the community under study | Tradeoff | Fraction = from tradeoff() function pfba = True min_growth = 0 solver = gurobi |
OptCom | Maximizes community growth rate (as described above) by maximizing each species growth at a steady state using a series of strategies (lagrangian, minimization of metabolic adjustment (MOMA), linear MOMA (LMOMA)) | Yes | Growth rates | Does not assume that all taxa have the same growth rate; allows for taxon-specific dilution rates | lMoma, Moma, Original | Strategy = (moma, lmoma, original) min_growth = 0 solver = gurobi | ||
MMT | List of GEMs handled in pairwise combinations | Pairwise | Maximizes biomass functions of both species simultaneously using a merged model of the 2 GEMs | Yes | Growth rates, interaction type | User-provided threshold defining what is considered a significant difference between growth rate in mono- and co-culture |  | sigD = 0.1 c = 400 u = 0 solver = gurobi |