Pairwise interactions and serial bottlenecks help explain species composition in a multi-species microbial community

Abstract

Characterizing the processes that drive microbial community assembly remains a key challenge in ecology. Several recent studies have argued that pairwise interactions may be insufficient to explain co-occurrence patterns in complex microbial communities, but most such studies have focused on synthetic communities not found in nature or microbes grown in contexts that differ widely from their natural environment. Moreover, most models of pairwise interactions rely on equilibrium assumptions that are not relevant to all natural communities, such as gut microbiomes or species in fluctuating environments. Inclusion of appropriate demographic factors into models of pairwise interactions could be a potential approach to better capture patterns of community assembly. In this study, we investigated whether multi-species co-occurrence patterns can be predicted from pairwise interactions for microbes isolated from sourdough starters. Interaction parameters inferred from pairwise growth trajectories were suggestive of widespread coexistence between pairs of microbes in our species pool. In communities of up to nine species, most species presence and relative abundance could be reliably predicted based on a model of pairwise interactions. The inclusion of nonequilibrium demography in our model further improved the accuracy of our pairwise model. Our work contributes to the broader debate on the processes underlying community assembly by showing that pairwise interactions are predictive of community structure in a system of moderate species complexity.