Extended Data Fig. 10: Modeling framework was able to predict assembly compositions and interrogate interactions in the complex medium mGAM.
From: Resource competition predicts assembly of gut bacterial communities in vitro
(a) Monoculture yields in mGAM differed from those in BHI, particularly for the Bacteroidetes, which exhibited substantially larger yields in mGAM. Shown are mean values across replicates. (b) The distribution of resource competition residues in mGAM was centered about zero, as in BHI (Fig. 1d). (c) Pairwise overlaps in metabolomic profiles in mGAM and BHI were correlated (ρ = 0.66). The pairwise overlap between the ordered species pair (i, j) was defined as the number of metabolomic features depleted by both species divided by the number depleted by species i. Shown are all 210 ordered pairs, colored according to species i. (d) Yield in monoculture (left) and pairwise spent-media experiments (right) was correlated with feature counts for experiments not involving the four Bacteroidetes (ρ = 0.54). Pairwise spent-media experiments involving the four Bacteroidetes are not shown. (e) Incorporation of additional interactions significantly and specifically improved model performance in mGAM. Shown are box plots denoting the mean error (thick central mark), the 25th and 75th percentiles (box), and the extremes (dashed lines) across all assemblies tested for model predictions in BHI (orange; n = 185 assemblies) and mGAM (blue; n = 158 assemblies), parametrized using metabolomics and spent-media experiments in the corresponding media, as well as mean errors for the consumer-resource model in mGAM modified to incorporate Bt/Bu-Clostridia interactions (dark blue) or with ubiquitous Clostridia inhibition (light blue). (f) The 5 Clostridia species exhibited no detectable growth in Bt- or Bu-spent media. Each panel shows the growth curve of a species in monoculture (solid line) and in pairwise spent media (dotted lines). The color of the solid line denotes the species grown in each panel. The color of the dotted lines denotes the species that generated the spent media. Gray dotted lines show growth curves in all other spent media.
