Abstract
A major open question in microbial community ecology is whether we can predict how the components of a diet collectively determine the taxonomic composition of microbial communities. Motivated by this challenge, we investigate whether communities assembled in pairs of nutrients can be predicted from those assembled in every single nutrient alone. We find that although the null, naturally additive model generally predicts well the family-level community composition, there exist systematic deviations from the additive predictions that reflect generic patterns of nutrient dominance at the family level. Pairs of more-similar nutrients (e.g. two sugars) are on average more additive than pairs of more dissimilar nutrients (one sugar-one organic acid). Furthermore, sugar-acid communities are generally more similar to the sugar than the acid community, which may be explained by family-level asymmetries in nutrient benefits. Overall, our results suggest that regularities in how nutrients interact may help predict community responses to dietary changes.
Highlights
Understanding how the components of a complex biological system combine to produce the system’s properties and functions is a fundamental question in biology
To investigate whether communities assembled in pairs of nutrients can be predicted from those assembled in every single nutrient alone, we must first develop a quantitative null model that predicts community composition in a mixed nutrient environment in the case where each nutrient recruits species independently
In order to formulate the null expectation for independently acting nutrients, let us consider a simple environment consisting of two unconnected demes where two bacterial species, A and B, can grow together
Summary
Understanding how the components of a complex biological system combine to produce the system’s properties and functions is a fundamental question in biology. Despite the important insights provided by both of these studies, we do not yet have a general quantitative understanding of how specific nutrients combine together to shape the composition of self-assembled communities (Pacheco and Segre, 2020). Motivated by this challenge, here we use an enrichment community approach (i.e. where natural microbial communities are grown in a defined growth medium under well-controlled lab conditions) to systematically investigate whether the assembly of enrichment microbial communities in a collection of defined nutrient mixes could be predicted from the communities that assembled in each of the single nutrients in isolation
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