The MPLEx Protocol for Multi-omic Analyses of Soil Samples

Journal Article · Mon Jan 01 04:00:00 EST 2018 · Journal of Visualized Experiments

DOI:https://doi.org/10.3791/57343· OSTI ID:1455290

Nicora, Carrie D.; Burnum-Johnson, Kristin E.; Nakayasu, Ernesto S.; Casey, Cameron P.; White, Richard A.; Roy Chowdhury, Taniya; Kyle, Jennifer E.; Kim, Young-Mo; Smith, Richard D.; Metz, Thomas O.; Jansson, Janet K.; Baker, Erin S.

Mass spectrometry (MS)-based integrated metaproteomic, metabolomic and lipidomic (multi-omic) studies are transforming our ability to understand and characterize microbial communities in environmental and biological systems. These measurements are even enabling enhanced analyses of complex soil microbial communities, which are the most complex microbial systems known to date. Multi-omic analyses, however, do have sample preparation challenges since separate extractions are typically needed for each omic study, thereby greatly amplifying the preparation time and amount of sample required. To address this limitation, a 3-in-1 method for simultaneous metabolite, protein, and lipid extraction (MPLEx) from the exact same soil sample was created by adapting a solvent-based approach. This MPLEx protocol has proven to be simple yet robust for many sample types and even when utilized for limited quantities of complex soil samples. The MPLEx method also greatly enabled the rapid multi-omic measurements needed to gain a better understanding of the members of each microbial community, while evaluating the changes taking place upon biological and environmental perturbations.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 1455290
• Report Number(s): PNNL-SA-129344; 48680; 48135; 400412000
• Journal Information: Journal of Visualized Experiments, Journal Name: Journal of Visualized Experiments Journal Issue: 135; ISSN 1940-087X; ISSN JVEOA4
• Publisher: MyJoVE Corp.
• Country of Publication: United States
• Language: English

Related Subjects

Environmental Molecular Sciences Laboratory