MetaFlowTrain

Metabolic fluxes between cells, organisms, or communities drive ecosystem assembly and functioning and explain high-level biological organization. Exometabolite-mediated inter-organismal communication, however, remains poorly described due to the lack of systems exclusively developed to address this technical challenge. Here, we present MetaFlowTrain, an easy-to-built, cheap, semi-high throughput, modular, and versatile fluidic system in which multiple metabolic inputs (synthetic or host-derived media) can be flushed at adjustable flow rates into gnotobiotic microchambers that can accommodate a wide-range of micro-organisms, ranging from bacteria to small eukaryotes. These gnotobiotic microchambers can be used alone or connected in series to create microchamber trains within which metabolites, but not organisms, directionally travel from chamber-to-chamber to modulate organism growth. We provide evidence that plant-microbe-microbe metabolic interactions modulate microbiota assembly and host phenotypes but also discuss the broader relevance of the system for studying within-ecosystem metabolic exchanges.