Extended Data Fig. 7: Characterizations of the Keio auxotrophic (a & b) and non-auxotrophic (c) communities.

a. Community growth response to amino acid concentrations and initial density. Collective growth demonstrates the presence of positive interactions among 47 Keio auxotroph strains. With no casamino acids added (the darkest trace) and 0.0002% of casamino acid, the auxotroph Keio community shows no detectable growth at 48 hours in M9 medium at 30^oC despite having an initial density above 0. However, with higher initial cell densities, the community began to grow, which is a typical behavior of cooperative communities. The data are represented as mean with error bars representing standard deviations across 7 replicate wells (N = 7). From the darkest to lightest, the lines casamino acid concentrations of 0%, 0.0002%, 0.001%, 0.005%, 0.02%, and 0.1%. b. The distribution of OD600 of each well at different casamino acid concentrations and partitioning levels. As expected, there is systematic increase in OD600 with increasing casamino acid concentrations (labeled at each row). Based on the initial cell density and Poisson distribution, 96 and 384-well plates are almost always are seeded with at least one cell in each well. However, at low casamino concentrations (0.0002% and 0.001%), bimodal distributions occur at 96 and 384-well plates indicating that the initial community compositions and their interactions play a crucial role in the growth of a strain. At the 1536 partitioning level, high casamino acid concentrations (0.1% and 0.02%) also show bi-modal distributions, which is expected due to a probability of ~30% wells being empty at a \(\lambda = 1.2\).c. Increased diversity with a 94-member community dominated by negative interactions. The strains were randomly selected from the Keio collection with auxotrophic strains excluded. Since all strains share the same genetic background, strong negative interactions are expected due to competition for nutrients and space.

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