PNNL

Abstract

Communication within the microbiome occurs through an immense diversity of small molecules. Capturing these microbial interactions is a significant challenge due to the complexity of the exometabolome and its sensitivity to environmental stimuli. Traditional methods for acquiring exometabolomics data from interacting microorganisms are limited by their low throughput or lack of sampling depth. To address this challenge, we introduce subtapping, a technique for tapping into extracellular metabolites that are being transferred through the growth substrate during coculture. The 3D printed SubTap platform captures the exometabolome in an agar compartment that connects physically separated growth chambers. This facilitates replicable and quick detection of exometabolites via direct infusion mass spectrometry analysis. Using bacterial isolates from the soil, we characterize the effects of growth medium, growth duration, and mixed versus unmixed coculturing on the exometabolome. Finally, we demonstrate SubTap's versatility by interrogating microbial interactions in multi-cultures with up to four species.