Abstract
A major open question in microbiome research is whether we can predict how the components of a diet collectively determine the taxonomic composition of microbial communities. Motivated by this challenge, here we ask whether communities assembled in a mixed nutrient environment can be predicted from those assembled in every single nutrient in isolation. To that end, we first formulate a quantitative null model of community assembly in a mixture of nutrients that recruit species independently. We then test the model predictions by assembling replicate communities in synthetic environments that contain either a pair of nutrients, or each nutrient in isolation. We find that the null, naturally additive model generally predicts well the family-level community composition. However, we also identify systematic deviations from the additive predictions that reflect generic patterns of nutrient dominance at the family-level of taxonomy. Pairs of more-similar nutrients (e.g. two sugars) are on average more additive than pairs of more dissimilar nutrients (e.g. one sugar and one organic acid). A simple dominance rule emerges, where we find that sugars generally dominate organic acids. This simple dominance rule extends to most families and most sugar-organic acid pairs in our experiment. Our results suggest that regularities in the ways nutrients interact may help us predict how microbial communities respond to changes in nutrient composition.
Competing Interest Statement
The authors have declared no competing interest.