Algorithms

SMETANA implements several algorithms to analyse cross-feeding interactions in microbial communities. These have been describe in Zelezniak et al, PNAS (2015). Please read the paper for a more detailed explanation.

Global

SMETANA includes two algorithms that analyse global properties of a community:

  • MRO (metabolic resource overlap): calculates how much the species compete for the same metabolites.
  • MIP (metabolic interaction potential): calculates how many metabolites the species can share to decrease their dependency on external resources.

Detailed

SMETANA includes several scores to characterize individual interactions in a community. This includes:

  • SCS (species coupling score): measures the dependency of one species in the presence of the others to survive
  • MUS (metabolite uptake score): measures how frequently a species needs to uptake a metabolite to survive
  • MPS (metabolite production score): measures the ability of a species to produce a metabolite
  • SMETANA: the individual smetana score is a combination of the 3 scores above, it gives a measure of certainty on a cross-feeding interaction (species A receives metabolite X from species B).