Eshima Jarrett, Pennington Taylor R, Abdellatif Youssef, Ponce Olea Angela, Lusk Joel F, Ambrose Benjamin D, Marschall Ethan, Miranda Christopher, Phan Paula, Aridi Christina, Smith Barbara S
School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, 85287, USA.
School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, 85287, USA.
Commun Eng. 2025 Sep 24;4(1):162. doi: 10.1038/s44172-025-00364-y.
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.
挥发性有机化合物（VOCs）是生物体代谢组中具有重要生物学意义的一个子集，但在实践中，用于分析这些小分子的体外技术差异很大，这限制了研究结果的解释。在此，我们展示了一种经过设计的培养工具，称为“生物穹顶”，旨在通过整合动态顶空采样方法来提高内源性分析物的回收率，该方法用于从生物培养物中回收挥发性有机化合物。我们利用计算建模和哺乳动物细胞培养的荧光成像来验证该设备用于体外挥发性代谢组学的功能。借助综合二维气相色谱与飞行时间质谱联用技术以及我们工具提供的增强采样能力，我们鉴定出14种在培养基中未发现或并非由采样方法外源产生的具有统计学意义的挥发性有机化合物，其中四种此前未在体外报道过。为证明其在哺乳动物细胞培养之外的适用性，我们评估了氨苄青霉素抗性DH5α大肠杆菌在对数生长期和稳定期整个生长过程中挥发性有机化合物的产生情况。我们鉴定出19种支持内源性产生的化合物，其中两种此前未与大肠杆菌相关联，即3-辛酮和3-十三烷酮。我们的研究结果强调了生物穹顶在体外挥发性代谢组学方面的改进能力。
