Quo Vadis Caenorhabditis elegans Metabolomics—A Review of Current Methods and Applications to Explore Metabolism in the Nematode

Abstract

Metabolomics and lipidomics recently gained interest in the model organism Caenorhabditis elegans (C. elegans). The fast development, easy cultivation and existing forward and reverse genetic tools make the small nematode an ideal organism for metabolic investigations in development, aging, different disease models, infection, or toxicology research. The conducted type of analysis is strongly depending on the biological question and requires different analytical approaches. Metabolomic analyses in C. elegans have been performed using nuclear magnetic resonance (NMR) spectroscopy, direct infusion mass spectrometry (DI-MS), gas-chromatography mass spectrometry (GC-MS) and liquid chromatography mass spectrometry (LC-MS) or combinations of them. In this review we provide general information on the employed techniques and their advantages and disadvantages in regard to C. elegans metabolomics. Additionally, we reviewed different fields of application, e.g., longevity, starvation, aging, development or metabolism of secondary metabolites such as ascarosides or maradolipids. We also summarised applied bioinformatic tools that recently have been used for the evaluation of metabolomics or lipidomics data from C. elegans. Lastly, we curated metabolites and lipids from the reviewed literature, enabling a prototypic collection which serves as basis for a future C. elegans specific metabolome database.

Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation

“…Here, untargeted metabolomics data could be used to help to improve the GSMNs by identifying missing metabolites and filling missing metabolic pathways. For example, metabolites predicted from the WormJam GSMN have been compared against detected metabolites in the nematode Caenorhabditis elegans (C. elegans) in different studies ( Salzer and Witting, 2021 ). Interestingly, the overlap of detected and predicted metabolites was rather modest (less than 40%).…”

Glucose-Potentiated Amikacin Killing of Cefoperazone/Sulbactam Resistant Pseudomonas aeruginosa

“…They have shown that oxaloacetate-phosphoenolpyruvate-pyruvate-AcCoA-citrate and malate-pyruvate-AcCoA-citrate occur, but the major flux is from phosphoenolpyruvate to pyruvate to AcCoA, with appreciable amount of carbon going to oxalacetate from pyruvate ( Kohlstedt and Wittmann, 2019 ), which is consistent with oxaloacetate instead of AcCoA as a fuel in the P cycle ( Su et al, 2018 ). On the other hand, GC–MS, NMR, and UPLC-MS are three main analytical technologies supporting metabolomics with their own advantages and disadvantages ( Peng et al, 2015a ; Salzer and Witting, 2021 ). In our case, the reduced glycolysis, pyruvate cycle and electron transport chain was identified by GC–MS and then validated by qRT-PCR or/and enzyme measurement, which is further supported by NADH, PMF and ATP.…”

Understanding Inborn Errors of Metabolism through Metabolomics

“…Additionally, they have a short generation time and short lifespan and their main route of reproduction is through self-fertilization. This hermaphroditic reproduction leads to low genetic variation [ 52 ]. Although not all metabolic pathways are the same as in humans, the most important ones such as glycolysis, the TCA cycle, and PPP are conserved in this animal model.…”