Microbial coexistence through chemical-mediated interactions

May 3, 2019
Lori Niehaus, Ian Boland, Minghao Liu, Kevin Chen, David Fu, Catherine Henckel, Kaitlin Chaung, Suyen Espinoza Miranda, Samantha Dyckman, Matthew Crum, Sandra Dedrick, Wenying Shou, Babak Momeni
Nature Communications

Abstract
Many microbial functions happen within communities of interacting species. Explaining how species with disparate growth rates can coexist is important for applications such as manipulating host-associated microbiota or engineering industrial communities. Here, we ask how microbes interacting through their chemical environment can achieve coexistence in a continuous growth setup (similar to an industrial bioreactor or gut microbiota) where external resources are being supplied. We formulate and experimentally constrain a model in which mediators of interactions (e.g. metabolites or waste-products) are explicitly incorporated. Our model highlights facilitation and self-restraint as interactions that contribute to coexistence, consistent with our intuition. When interactions are strong, we observe that coexistence is determined primarily by the topology of facilitation and inhibition influences not their strengths. Importantly, we show that consumption or degradation of chemical mediators moderates interaction strengths and promotes coexistence. Our results offer insights into how to build or restructure microbial communities of interest. Read more