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

Author

Listed:
  • 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
    Max Planck Institute for Plant Breeding Research)

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.

Suggested Citation

  • Guillaume Chesneau & Johannes Herpell & Sarah Marie Wolf & Silvina Perin & Stéphane Hacquard, 2025. "MetaFlowTrain: a highly parallelized and modular fluidic system for studying exometabolite-mediated inter-organismal interactions," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58530-x
    DOI: 10.1038/s41467-025-58530-x
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    1. Felix Getzke & Lei Wang & Guillaume Chesneau & Nils Böhringer & Fantin Mesny & Nienke Denissen & Hidde Wesseler & Priscilla Tijesuni Adisa & Michael Marner & Paul Schulze-Lefert & Till F. Schäberle & , 2024. "Physiochemical interaction between osmotic stress and a bacterial exometabolite promotes plant disease," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    2. Yang Bai & Daniel B. Müller & Girish Srinivas & Ruben Garrido-Oter & Eva Potthoff & Matthias Rott & Nina Dombrowski & Philipp C. Münch & Stijn Spaepen & Mitja Remus-Emsermann & Bruno Hüttel & Alice C., 2015. "Functional overlap of the Arabidopsis leaf and root microbiota," Nature, Nature, vol. 528(7582), pages 364-369, December.
    3. Fantin Mesny & Shingo Miyauchi & Thorsten Thiergart & Brigitte Pickel & Lea Atanasova & Magnus Karlsson & Bruno Hüttel & Kerrie W. Barry & Sajeet Haridas & Cindy Chen & Diane Bauer & William Andreopou, 2021. "Genetic determinants of endophytism in the Arabidopsis root mycobiome," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    4. Jonathan M. Levine & Jordi Bascompte & Peter B. Adler & Stefano Allesina, 2017. "Beyond pairwise mechanisms of species coexistence in complex communities," Nature, Nature, vol. 546(7656), pages 56-64, June.
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