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MetaboLights MTBLS525 - GNPS A synthetic community system for probing microbial interactions driven by exometabolites

ABSTRACT: Despite that most microorganisms live as part of community, we have modest knowledge about the interactions among microbial community members in nature, and the implications of those interactions for emergent community properties or ecosystem-relevant functions. To facilitate advances in understanding microbial interactions, we describe a straightforward synthetic community system for interrogating the extracellular interactions among microbial community members. The laboratory-scale system physically separates microbial populations within the community, but allows for chemical interactions via a shared media reservoir. Community goods, including small molecules, extracellular enzymes, and antibiotics, can be assayed using sensitive mass spectrometry, and community member outcomes can be assayed, for example, using flow cytometry, biomass measurements, and transcript analyses. The synthetic community design allows for determining the causes and consequences of community diversity and functional outcomes given manipulation of community membership or structure, abiotic stressors, or temporal dynamics. Because it is versatile to accommodate any artificial or environmental microbiome members, scalable to high-throughput capacity, flexible to an array of experimental designs, and accessible to a variety of laboratories because no specialized or costly components are required, this synthetic community system has the potential to practically advance knowledge of microbial interactions within both natural and artificial communities.

INSTRUMENT(S): Xevo G2 Tof|1001784

ORGANISM(S): Burkholderia Thailandensis|57975

SUBMITTER: John Chodkowski

PROVIDER: MSV000085860 | GNPS | Fri Jul 31 07:03:00 BST 2020

REPOSITORIES: GNPS

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A synthetic community system for probing microbial interactions driven by exometabolites

Project description:Despite that most microorganisms live as part of community, we have modest knowledge about the interactions among microbial community members in nature, and the implications of those interactions for emergent community properties or ecosystem-relevant functions. To facilitate advances in understanding microbial interactions, we describe a straightforward synthetic community system for interrogating the extracellular interactions among microbial community members. The laboratory-scale system physically separates microbial populations within the community, but allows for chemical interactions via a shared media reservoir. Community goods, including small molecules, extracellular enzymes, and antibiotics, can be assayed using sensitive mass spectrometry, and community member outcomes can be assayed, for example, using flow cytometry, biomass measurements, and transcript analyses. The synthetic community design allows for determining the causes and consequences of community diversity and functional outcomes given manipulation of community membership or structure, abiotic stressors, or temporal dynamics. Because it is versatile to accommodate any artificial or environmental microbiome members, scalable to high-throughput capacity, flexible to an array of experimental designs, and accessible to a variety of laboratories because no specialized or costly components are required, this synthetic community system has the potential to practically advance knowledge of microbial interactions within both natural and artificial communities.

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A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites

Project description:Though most microorganisms live within a community, we have modest knowledge about microbial interactions and their implications for community properties and ecosystem functions. To advance understanding of microbial interactions, we describe a straightforward synthetic community system that can be used to interrogate exometabolite interactions among microorganisms. The filter plate system (also known as the Transwell system) physically separates microbial populations, but allows for chemical interactions via a shared medium reservoir. Exometabolites, including small molecules, extracellular enzymes, and antibiotics, are assayed from the reservoir using sensitive mass spectrometry. Community member outcomes, such as growth, productivity, and gene regulation, can be determined using flow cytometry, biomass measurements, and transcript analyses, respectively. The synthetic community design allows for determination of the consequences of microbiome diversity for emergent community properties and for functional changes over time or after perturbation. Because it is versatile, scalable, and accessible, this synthetic community system has the potential to practically advance knowledge of microbial interactions that occur within both natural and artificial communities. See publications: https://journals.asm.org/doi/10.1128/mSystems.00129-17 and https://journals.asm.org/doi/10.1128/mSystems.00493-20 and https://www.biorxiv.org/content/10.1101/2021.09.05.459016v2.full. The work (proposal:https://doi.org/10.46936/10.25585/60000724) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

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