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SubTap, a Versatile 3D Printed Platform for Eavesdropping on Extracellular Interactions.

Caroline M C Birer-Williams1,2, Rosalie K Chu3, Christopher R Anderton3

  • 1Biomolécules et Biotechnologies Végétales (BBV) EA 2106, Université de Tours, Tours, France.

Msystems
|August 24, 2021
PubMed
Summary

We developed SubTap, a 3D-printed platform for high-throughput exometabolomics. This technique enables efficient analysis of microbial communication and metabolite transfer in cocultures, advancing microbiome research.

Keywords:
3D printingchemical ecologyexometabolomeintercellular communicationmetabolomicsmicrobiome

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Area of Science:

  • Microbiome research
  • Metabolomics
  • Microbial interaction analysis

Background:

  • Microbiome communication relies on diverse small molecules, but exometabolome complexity poses challenges for analysis.
  • Traditional methods for studying microbial interactions are low-throughput and lack sampling depth.
  • High-throughput interrogation of microbial exometabolomes is crucial for understanding microbiome roles in health and environment.

Purpose of the Study:

  • To introduce a novel, high-throughput technique called subtapping for analyzing extracellular metabolites during microbial coculture.
  • To present the SubTap platform, a 3D-printed, 96-well plate-like device engineered for efficient exometabolomic data acquisition.
  • To demonstrate the versatility and applicability of SubTap in characterizing microbial interactions and exometabolomes under various conditions.

Main Methods:

  • Engineered a 3D-printed coculturing platform (SubTap) with physically separated growth chambers connected by an agar compartment.
  • Utilized subtapping to capture extracellular metabolites transferred through the growth substrate during coculture.
  • Employed direct infusion mass spectrometry for rapid and replicable detection of exometabolites.

Main Results:

  • The SubTap platform enables high-throughput, scalable, and customizable coculturing compatible with mass spectrometry.
  • Subtapping successfully captured and analyzed exometabolites from soil bacterial isolates, revealing effects of growth medium and duration.
  • Demonstrated the platform's capability to interrogate microbial interactions in multicultures of up to four strains.

Conclusions:

  • Subtapping, facilitated by the SubTap platform, offers a significant advancement for high-throughput exometabolomic studies.
  • The developed technique addresses limitations of traditional methods, enabling deeper insights into microbial communication.
  • SubTap provides an open-source, cost-effective, and versatile solution for large-scale microbiome interrogations.