MetaFlowTrain: a highly parallelized and modular fluidic system for studying exometabolite-mediated inter-organismal interactions

Guillaume Chesneau, Johannes Herpell, Sarah Marie Wolf, Silvina Perin and Stéphane Hacquard ()
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Guillaume Chesneau: Max Planck Institute for Plant Breeding Research
Johannes Herpell: Max Planck Institute for Plant Breeding Research
Sarah Marie Wolf: Max Planck Institute for Plant Breeding Research
Silvina Perin: Max Planck Institute for Plant Breeding Research
Stéphane Hacquard: Max Planck Institute for Plant Breeding Research

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract Metabolic fluxes between cells, organisms, or communities drive ecosystem assembly and functioning and explain higher-level biological organization. Exometabolite-mediated inter-organismal interactions, however, remain poorly described due to technical challenges in measuring these interactions. Here, we present MetaFlowTrain, an easy-to-assemble, cheap, semi-high-throughput, and modular fluidic system in which multiple media can be flushed at adjustable flow rates into gnotobiotic microchambers accommodating diverse micro-organisms, ranging from bacteria to small eukaryotes. These microchambers can be used alone or connected in series to create microchamber trains within which metabolites, but not organisms, directionally travel between microchambers to modulate organismal growth. Using MetaFlowTrain, we uncover soil conditioning effects on synthetic community structure and plant growth, and reveal microbial antagonism mediated by exometabolite production. Our study highlights MetaFlowTrain as a versatile system for investigating plant-microbe-microbe metabolic interactions. We also discuss the system´s potential to discover metabolites that function as signaling molecules, drugs, or antimicrobials across various systems.

Date: 2025
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DOI: 10.1038/s41467-025-58530-x

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