de Raad Markus, Li Yifan V, Kuehl Jennifer V, Andeer Peter F, Kosina Suzanne M, Hendrickson Andrew, Saichek Nicholas R, Golini Amber N, Han La Zhen, Wang Ying, Bowen Benjamin P, Deutschbauer Adam M, Arkin Adam P, Chakraborty Romy, Northen Trent R
Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States.
Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Front Microbiol. 2022 May 25;13:855331. doi: 10.3389/fmicb.2022.855331. eCollection 2022.
Exometabolomics is an approach to assess how microorganisms alter, or react to their environments through the depletion and production of metabolites. It allows the examination of how soil microbes transform the small molecule metabolites within their environment, which can be used to study resource competition and cross-feeding. This approach is most powerful when used with defined media that enable tracking of all metabolites. However, microbial growth media have traditionally been developed for the isolation and growth of microorganisms but not metabolite utilization profiling through Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS). Here, we describe the construction of a defined medium, the Northen Lab Defined Medium (NLDM), that not only supports the growth of diverse soil bacteria but also is defined and therefore suited for exometabolomic experiments. Metabolites included in NLDM were selected based on their presence in R2A medium and soil, elemental stoichiometry requirements, as well as knowledge of metabolite usage by different bacteria. We found that NLDM supported the growth of 108 of the 110 phylogenetically diverse (spanning 36 different families) soil bacterial isolates tested and all of its metabolites were trackable through LC-MS/MS analysis. These results demonstrate the viability and utility of the constructed NLDM medium for growing and characterizing diverse microbial isolates and communities.
胞外代谢组学是一种通过代谢物的消耗和产生来评估微生物如何改变其环境或对环境做出反应的方法。它能够研究土壤微生物如何转化其环境中的小分子代谢物，可用于研究资源竞争和交叉喂养。当与能够追踪所有代谢物的特定培养基一起使用时，这种方法最为有效。然而，传统上微生物生长培养基是为微生物的分离和生长而开发的，并非用于通过液相色谱串联质谱法（LC-MS/MS）进行代谢物利用分析。在此，我们描述了一种特定培养基——诺森实验室特定培养基（NLDM）的构建，它不仅支持多种土壤细菌的生长，而且成分明确，因此适用于胞外代谢组学实验。NLDM中包含的代谢物是根据它们在R2A培养基和土壤中的存在情况、元素化学计量学要求以及不同细菌对代谢物的利用知识来选择的。我们发现，NLDM支持所测试的110种系统发育多样（涵盖36个不同科）的土壤细菌分离株中的108种生长，并且其所有代谢物都可通过LC-MS/MS分析进行追踪。这些结果证明了构建的NLDM培养基用于培养和表征多种微生物分离株及群落的可行性和实用性。
