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Metabolites
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Metabolomics 2019
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Metabolomics 2019

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Advances in Metabolomics".

Deadline for manuscript submissions: closed (31 October 2019) | Viewed by 43849

Special Issue Editors

Prof. Dr. Oliver A. H. Jones

E-Mail Website
Guest Editor
Biosciences and Food Technology, RMIT University, Melbourne, VIC 3000, Australia
Interests: analytical chemistry; biochemistry; metabolomics; NMR; water and environmental technology
Dr. Horst Joachim Schirra

E-Mail Website
Guest Editor
Centre for Advanced Imaging, University of Queensland, Brisbane, QLD 4072, Australia
Interests: NMR spectroscopy; metabolomics; C. elegans; genome-scale models; metabolic regulation; gasotransmitters; mitochondrial metabolism; hypometabolism; foodomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The 15th International Conference of the Metabolomics Society is the continuation of a conference series that has been held annually since 2005. It is the official meeting of the Metabolomics Society and the largest international metabolomics conference worldwide. It brings together all the major international organizations involved in metabolomics, with topics including metabolite identification, metabolic desease, food science, plant and microbial biology, environment science and toxicology, as well as all the new developoments in analytical technologies and bioinformatics and data processing.

For this Special Issue, we particularly, but not exclusively, welcome papers presented at or resulting from the 15th International Conference of the Metabolomics Society held in The Hague, The Netherlands, in June 2019, with a focus on any topic relevant to metabolomic science.

More information about the 15th International Conference of the Metabolomics Society can be found at: http://metabolomics2019.org/

We look forward to reading your papers! 

Best regards

Assoc. Prof. Oliver A.H. Jones
Dr. Horst Joachim Schirra
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • metabolite identification
  • metabolic desease/medicine
  • environmental science and toxicology
  • novel analytical technologies, instruments and applications
  • NMR Spectroscopy
  • Chromatography and Separation Science
  • Mass Spectrometry
  • Microbiology
  • Model organisms
  • Bioinformatics
  • Systems biology and metabolic modelling
  • Data processing

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Published Papers (7 papers)

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Research

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15 pages, 1785 KiB  
Article
Ammonium Fluoride as Suitable Additive for HILIC-Based LC-HRMS Metabolomics
by Luca Narduzzi, Anne-Lise Royer, Emmanuelle Bichon, Yann Guitton, Corinne Buisson, Bruno Le Bizec and Gaud Dervilly-Pinel
Metabolites 2019, 9(12), 292; https://doi.org/10.3390/metabo9120292 - 27 Nov 2019
Cited by 18 | Viewed by 6553
Abstract
Hydrophilic Interaction Liquid Chromatography (HILIC) chromatography is widely applied in metabolomics as a complementary strategy to reverse phase chromatography. Nevertheless, it still faces several issues in terms of peak shape and compounds ionization, limiting the automatic de-convolution and data semi-quantification performed through dedicated [...] Read more.
Hydrophilic Interaction Liquid Chromatography (HILIC) chromatography is widely applied in metabolomics as a complementary strategy to reverse phase chromatography. Nevertheless, it still faces several issues in terms of peak shape and compounds ionization, limiting the automatic de-convolution and data semi-quantification performed through dedicated software. A way to improve the chromatographic and ionization performance of a HILIC method is to modify the electrostatic interactions of the analytes with both mobile and stationary phases. In this study, using a ZIC-HILIC chromatographic phase, we evaluated the performance of ammonium fluoride (AF) as additive salt, comparing its performance to ammonium acetate (AA). Three comparative criteria were selected: (1) identification and peak quality of 34 standards following a metabolomics-specific evaluation approach, (2) an intraday repeatability test with real samples and (3) performing two real metabolomics fingerprints with the AF method to evaluate its inter-day repeatability. The AF method showed not only higher ionization efficiency and signal-to-noise ratio but also better repeatability and robustness than the AA approach. A tips and tricks section is then added, aiming at improving method replicability for further users. In conclusion, ammonium fluoride as additive salt presents several advantages and might be considered as a step forward in the application of robust HILIC methods in metabolomics. Full article
(This article belongs to the Special Issue Metabolomics 2019)
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12 pages, 2667 KiB  
Article
Heat Stress-Induced Metabolic Remodeling in Saccharomyces cerevisiae
by Daqiang Pan, Nils Wiedemann and Bernd Kammerer
Metabolites 2019, 9(11), 266; https://doi.org/10.3390/metabo9110266 - 5 Nov 2019
Cited by 16 | Viewed by 4728
Abstract
Yeast cells respond to heat stress by remodeling their gene expression, resulting in the changes of the corresponding proteins and metabolites. Compared to the intensively investigated transcriptome and proteome, the metabolic response to heat stress is not sufficiently characterized. Mitochondria have been recognized [...] Read more.
Yeast cells respond to heat stress by remodeling their gene expression, resulting in the changes of the corresponding proteins and metabolites. Compared to the intensively investigated transcriptome and proteome, the metabolic response to heat stress is not sufficiently characterized. Mitochondria have been recognized to play an essential role in heat stress tolerance. Given the compartmentalization of the cell, it is not clear if the heat stress-induced metabolic response occurs in mitochondria or in the cytosol. Therefore, a compartment-specific metabolite analysis was performed to analyze the heat stress-induced metabolic response in mitochondria and the cytoplasm. In this work, the isolated mitochondria and the cytoplasm of yeast cells grown at permissive temperature and cells adapting to heat stress were subjected to mass spectrometry-based metabolomics. Over a hundred metabolites could be identified, covering amino acid metabolism, energy metabolism, arginine metabolism, purine and pyrimidine metabolism, and others. Highly accumulated citrulline and reduced arginine suggested remodeled arginine metabolism. A stable isotope-labeled experiment was performed to analyze the heat stress-induced metabolic remodeling of the arginine metabolism, identifying activated de novo ornithine biosynthesis to support arginine and spermidine synthesis. The short-term increased spermidine and trehalose suggest their important roles as heat stress markers. These data provide metabolic clues of heat stress-induced metabolic remodeling, which helps in understanding the heat stress response. Full article
(This article belongs to the Special Issue Metabolomics 2019)
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16 pages, 2665 KiB  
Article
Metabolite Changes in an Estuarine Annelid Following Sublethal Exposure to a Mixture of Zinc and Boscalid
by Georgia M. Sinclair, Allyson L. O’Brien, Michael Keough, David P. de Souza, Saravanan Dayalan, Komal Kanojia, Konstantinos Kouremenos, Dedreia L. Tull, Rhys A. Coleman, Oliver A.H. Jones and Sara M. Long
Metabolites 2019, 9(10), 229; https://doi.org/10.3390/metabo9100229 - 15 Oct 2019
Cited by 14 | Viewed by 3379
Abstract
Environmental pollutants such as heavy metals and fungicides pose a serious threat to waterways worldwide. Toxicological assessment of such contaminants is usually conducted using single compound exposures, as it is challenging to understand the effect of mixtures on biota using standard ecotoxicological methods; [...] Read more.
Environmental pollutants such as heavy metals and fungicides pose a serious threat to waterways worldwide. Toxicological assessment of such contaminants is usually conducted using single compound exposures, as it is challenging to understand the effect of mixtures on biota using standard ecotoxicological methods; whereas complex chemical mixtures are more probable in ecosystems. This study exposed Simplisetia aequisetis (an estuarine annelid) to sublethal concentrations of a metal (zinc) and a fungicide (boscalid), both singly and as a mixture, for two weeks. Metabolomic analysis via gas and liquid chromatography-mass spectrometry was used to measure the stress response(s) of the organism following exposure. A total of 75 metabolites, including compounds contributing to the tricarboxylic acid cycle, the urea cycle, and a number of other pathways, were identified and quantified. The multiplatform approach identified distinct metabolomic responses to each compound that differed depending on whether the substance was presented singly or as a mixture, indicating a possible antagonistic effect. The study demonstrates that metabolomics is able to elucidate the effects and mode of action of contaminants and can identify possible outcomes faster than standard ecotoxicological endpoints, such as growth and reproduction. Metabolomics therefore has a possible future role in biomonitoring and ecosystem health assessments. Full article
(This article belongs to the Special Issue Metabolomics 2019)
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15 pages, 1045 KiB  
Article
Metabolic Effects of Dietary Glycerol Supplementation in Muscle and Liver of European Seabass and Rainbow Trout by 1H NMR Metabolomics
by Mariana Palma, Ludgero C. Tavares, João Rito, Luís F. Henriques, João G. Silva, Rodrigo Ozório, Miguel A. Pardal, Leonardo J. Magnoni and Ivan Viegas
Metabolites 2019, 9(10), 202; https://doi.org/10.3390/metabo9100202 - 27 Sep 2019
Cited by 21 | Viewed by 6567
Abstract
The sustainable growth of fish aquaculture will require the procurement of non-marine feed sources. Glycerol is a potential feed supplement whose metabolism may spare the catabolism of dietary amino acids, thereby extending the use of the feed protein to other physiological functions such [...] Read more.
The sustainable growth of fish aquaculture will require the procurement of non-marine feed sources. Glycerol is a potential feed supplement whose metabolism may spare the catabolism of dietary amino acids, thereby extending the use of the feed protein to other physiological functions such as growth. In the present study, the effects of dietary glycerol supplementation on the muscle and liver metabolomes of rainbow trout (Oncorhynchus mykiss) and European seabass (Dicentrarchus labrax) were evaluated. Fish juveniles were fed diets with 0%, 2.5%, and 5% glycerol. Muscle and liver aqueous fractions were extracted and 1H NMR spectra were acquired. Metabolite profiles derived from the 1H NMR signals were assessed using univariate and multivariate statistical analyses. The adenylate energy charge was determined in the muscle. For both species, the muscle metabolite profile showed more variability compared to that of the liver and was most perturbed by the 5.0% glycerol diet. For the liver metabolite profile, rainbow trout showed fewer differences compared to European seabass. No differences were observed in energy charge between experimental groups for either species. Thus, rainbow trout appeared to be less susceptible to tissue metabolite perturbations, compared to seabass, when the diet was supplemented with up to 5% glycerol. Full article
(This article belongs to the Special Issue Metabolomics 2019)
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19 pages, 5331 KiB  
Article
2-Deoxy-d-Glucose-Induced Metabolic Alteration in Human Oral Squamous SCC15 Cells: Involvement of N-Glycosylation of Axl and Met
by Naeun Lee, Won-Jun Jang, Ji Hae Seo, Sooyeun Lee and Chul-Ho Jeong
Metabolites 2019, 9(9), 188; https://doi.org/10.3390/metabo9090188 - 17 Sep 2019
Cited by 14 | Viewed by 4689
Abstract
One of the most prominent hallmarks of cancer cells is their dependency on the glycolytic pathway for energy production. As a potent inhibitor of glycolysis, 2-deoxy-d-glucose (2DG) has been proposed for cancer treatment and extensively investigated in clinical studies. Moreover, 2DG [...] Read more.
One of the most prominent hallmarks of cancer cells is their dependency on the glycolytic pathway for energy production. As a potent inhibitor of glycolysis, 2-deoxy-d-glucose (2DG) has been proposed for cancer treatment and extensively investigated in clinical studies. Moreover, 2DG has been reported to interfere with other biological processes including glycosylation. To further understand the overall effect of and metabolic alteration by 2DG, we performed biochemical and metabolomics analyses on oral squamous cell carcinoma cell lines. In this study, we found that 2DG more effectively reduced glucose consumption and lactate level in SCC15 cells than in SCC4 cells, which are less dependent on glycolysis. Coincidentally, 2DG impaired N-linked glycosylation of the key oncogenic receptors Axl and Met in SCC15 cells, thereby reducing the cell viability and colony formation ability. The impaired processes of glycolysis and N-linked glycosylation were restored by exogenous addition of pyruvate and mannose, respectively. Additionally, our targeted metabolomics analysis revealed significant alterations in the metabolites, including amino acids, biogenic amines, glycerophospholipids, and sphingolipids, caused by the impairment of glycolysis and N-linked glycosylation. These observations suggest that alterations of these metabolites may be responsible for the phenotypic and metabolic changes in SCC15 cells induced by 2DG. Moreover, our data suggest that N-linked glycosylation of Axl and Met may contribute to the maintenance of cancer properties in SCC15 cells. Further studies are needed to elucidate the roles of these altered metabolites to provide novel therapeutic targets for treating human oral cancer. Full article
(This article belongs to the Special Issue Metabolomics 2019)
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21 pages, 918 KiB  
Article
Targeted Clinical Metabolite Profiling Platform for the Stratification of Diabetic Patients
by Linda Ahonen, Sirkku Jäntti, Tommi Suvitaival, Simone Theilade, Claudia Risz, Risto Kostiainen, Peter Rossing, Matej Orešič and Tuulia Hyötyläinen
Metabolites 2019, 9(9), 184; https://doi.org/10.3390/metabo9090184 - 14 Sep 2019
Cited by 20 | Viewed by 5474
Abstract
Several small molecule biomarkers have been reported in the literature for prediction and diagnosis of (pre)diabetes, its co-morbidities, and complications. Here, we report the development and validation of a novel, quantitative method for the determination of a selected panel of 34 metabolite biomarkers [...] Read more.
Several small molecule biomarkers have been reported in the literature for prediction and diagnosis of (pre)diabetes, its co-morbidities, and complications. Here, we report the development and validation of a novel, quantitative method for the determination of a selected panel of 34 metabolite biomarkers from human plasma. We selected a panel of metabolites indicative of various clinically-relevant pathogenic stages of diabetes. We combined these candidate biomarkers into a single ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method and optimized it, prioritizing simplicity of sample preparation and time needed for analysis, enabling high-throughput analysis in clinical laboratory settings. We validated the method in terms of limits of detection (LOD) and quantitation (LOQ), linearity (R2), and intra- and inter-day repeatability of each metabolite. The method’s performance was demonstrated in the analysis of selected samples from a diabetes cohort study. Metabolite levels were associated with clinical measurements and kidney complications in type 1 diabetes (T1D) patients. Specifically, both amino acids and amino acid-related analytes, as well as specific bile acids, were associated with macro-albuminuria. Additionally, specific bile acids were associated with glycemic control, anti-hypertensive medication, statin medication, and clinical lipid measurements. The developed analytical method is suitable for robust determination of selected plasma metabolites in the diabetes clinic. Full article
(This article belongs to the Special Issue Metabolomics 2019)
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15 pages, 2098 KiB  
Review
Current Understanding of Methamphetamine-Associated Metabolic Changes Revealed by the Metabolomics Approach
by Minjeong Kim, Won-Jun Jang, Rupa Shakya, Boyeon Choi, Chul-Ho Jeong and Sooyeun Lee
Metabolites 2019, 9(10), 195; https://doi.org/10.3390/metabo9100195 - 20 Sep 2019
Cited by 23 | Viewed by 11431
Abstract
Metabolomics is a powerful tool used in the description of metabolic system perturbations caused by diseases or abnormal conditions, and it usually involves qualitative and/or quantitative metabolome determination, accompanied by bioinformatics assessment. Methamphetamine is a psychostimulant with serious abuse potential and due to [...] Read more.
Metabolomics is a powerful tool used in the description of metabolic system perturbations caused by diseases or abnormal conditions, and it usually involves qualitative and/or quantitative metabolome determination, accompanied by bioinformatics assessment. Methamphetamine is a psychostimulant with serious abuse potential and due to the absence of effective pharmacotherapy and a high recurrence potential, methamphetamine addiction is a grave issue. Moreover, its addiction mechanisms remain unclear, probably due to the lack of experimental models that reflect personal genetic variances and environmental factors determining drug addiction occurrence. The metabolic approach is only recently being used to study the metabolic effects induced by a variety of methamphetamine exposure statuses, in order to investigate metabolic disturbances related to the adverse effects and discover potential methamphetamine addiction biomarkers. To provide a critical overview of methamphetamine-associated metabolic changes revealed in recent years using the metabolomics approach, we discussed methamphetamine toxicity, applications of metabolomics in drug abuse and addiction studies, biological samples used in metabolomics, and previous studies on metabolic alterations in a variety of biological samples—including the brain, hair, serum, plasma, and urine—following methamphetamine exposure in animal studies. Metabolic alterations observed in animal brain and other biological samples after methamphetamine exposure were associated with neuronal and energy metabolism disruptions. This review highlights the significance of further metabolomics studies in the area of methamphetamine addiction research. These findings will contribute to a better understanding of metabolic changes induced by methamphetamine addiction progress and to the design of further studies targeting the discovery of methamphetamine addiction biomarkers and therapeutic targets. Full article
(This article belongs to the Special Issue Metabolomics 2019)
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