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bioRxiv · 10.1101/2022.05.30.494065

Resource competition predicts assembly of in vitro gut bacterial communities

Ho, P.-Y.·Nguyen, T. H.·Sanchez, J. M.·DeFelice, B. C.·Huang, K. C.
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Abstract

Members of microbial communities interact via a plethora of mechanisms, including resource competition, cross-feeding, and pH modulation. However, the relative contributions of these mechanisms to community dynamics remain uncharacterized. Here, we develop a framework to distinguish the effects of resource competition from other interaction mechanisms by integrating data from growth measurements in spent media, synthetic community assembly, and metabolomics with consumer-resource models. When applied to human gut commensals, our framework revealed that resource competition alone could explain most pairwise interactions. The resource-competition landscape inferred from metabolomic profiles of individual species predicted assembly compositions, demonstrating that resource competition is a dominant driver of in vitro community assembly. Moreover, the identification and incorporation of interactions other than resource competition, including pH-mediated effects and cross-feeding, improved model predictions. Our work provides an experimental and modeling framework to characterize and quantify interspecies interactions in vitro that should advance mechanistically principled engineering of microbial communities.

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Ho, P.-Y., Nguyen, T. H., Sanchez, J. M., DeFelice, B. C., Huang, K. C.. 2022-05-30. Resource competition predicts assembly of in vitro gut bacterial communities. https://doi.org/10.1101/2022.05.30.494065

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