Investigating the role of pairwise interactions in microbial community assembly

Using metabolic and ecological modeling, we investigate the question: is microbial co-occurrence in the human gut a result of pairwise interactions, or do higher order interactions play a signicant role? We perform model tting on data from pairwise bacterial growth experiments to produce deterministic and stochastic growth models for pairs and triplets of bacterial species. We measure the accuracy of the predictions given by the triplet models to asses the extent to which pairwise interaction parameters can explain triplet outcomes. We also use metabolic models to assess bacterial growth in pairs and triplets. Pairwise metabolic modeling can be used to determine interaction parameters between species, using for example dynamic ux balance analysis (dFBA). We compare the apparent pairwise interaction parameters derived from pair community models and triplet community models to determine whether or not constraint based metabolic modeling of communities depends strongly on only pairwise interactions, or if higher order interactions must be taken into account.