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

Summary

Scientists developed MetaFlowTrain, a system that allows them to study how different microorganisms communicate through chemical molecules they produce. The system uses tiny connected chambers with filters that let chemical signals pass between microbes but keep the organisms separated. This tool revealed that bacteria can inhibit fungal growth through their chemical products and showed how soil conditions affect microbial community structure and plant health.

Background

Metabolic interactions between organisms drive ecosystem assembly and functioning, but measuring exometabolite-mediated interactions remains technically challenging. Current methods for studying these interactions are limited by their inability to track dynamic changes over time, accommodate diverse organisms, or perform non-destructive sampling.

Objective

To develop MetaFlowTrain, a highly parallelized and modular fluidic system for studying exometabolite-mediated inter-organismal interactions. The system aims to enable continuous nutrient supply, precise metabolic flux control, and accommodation of phylogenetically diverse microorganisms while maintaining gnotobiotic compartmentalization.

Results

MetaFlowTrain successfully cultivated diverse bacteria, fungi, and microalgae while collecting exometabolites. Soil conditioning by plants and microbes altered community structure and exometabolite profiles affecting plant growth. Bacterial exometabolites strongly inhibited fungal growth, demonstrating that inhibition was mediated through exometabolite production rather than physical contact or medium consumption.

Conclusion

MetaFlowTrain provides a versatile, cost-effective platform for investigating exometabolite-mediated interactions across diverse biological systems. The system’s ability to control metabolic fluxes, maintain gnotobiotic conditions, and enable non-destructive sampling makes it valuable for discovering bioactive molecules and understanding inter-organismal communication.
  • Published in:Nature Communications,
  • Study Type:Methods/System Development,
  • Source: 10.1038/s41467-025-58530-x, PMID: 40210863
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