An engineered culture vessel and flow system to improve the in vitro analysis of volatile organic compounds

Volatile organic compounds (VOCs) are a biologically important subset of an organism's metabolome, yet in vitro techniques for the analysis of these small molecules vary substantially in practice, restricting the interpretation of study findings. Here, we present an engineered culture tool, termed the "Biodome", designed to enhance endogenous analyte recovery by integrating dynamic headspace sampling methodology for the recovery of VOCs from biological cultures. We validate the functionality of the device for in vitro volatile metabolomics utilizing computational modeling and fluorescent imaging of mammalian cell culture. Leveraging comprehensive two-dimensional gas chromatography coupled with a time-of-flight mass spectrometer and the enhanced sampling capabilities afforded by our tool, we identify 14 statistically significant VOCs not found in the media or exogenously derived from the sampling method, four of which have not been previously reported in vitro. To demonstrate applicability beyond mammalian cell culture, we assess the production of VOCs throughout the log and stationary phases of growth in ampicillin-resistant DH5α Escherichia coli. We identified 19 compounds with results supporting endogenous production, two of which had not previously associated with E. coli, 3-Octanone and 3-Tridecanone. Our findings emphasize the improved capabilities of the Biodome for in vitro volatile metabolomics.