Submit to Metabolites Review for Metabolites

Journal Menu

Journal Browser

Editor’s Choice Articles

Editor’s Choice articles are based on recommendations by the scientific editors of MDPI journals from around the world. Editors select a small number of articles recently published in the journal that they believe will be particularly interesting to readers, or important in the respective research area. The aim is to provide a snapshot of some of the most exciting work published in the various research areas of the journal.

Order results

Result details

Results per page

Show export options Show export options

Select all

Export citation of selected articles as:

35 pages, 15010 KiB

Open AccessEditor’s ChoiceProtocol

“Notame”: Workflow for Non-Targeted LC–MS Metabolic Profiling

by Anton Klåvus, Marietta Kokla, Stefania Noerman, Ville M. Koistinen, Marjo Tuomainen, Iman Zarei, Topi Meuronen, Merja R. Häkkinen, Soile Rummukainen, Ambrin Farizah Babu, Taisa Sallinen, Olli Kärkkäinen, Jussi Paananen, David Broadhurst, Carl Brunius and Kati Hanhineva

Metabolites 2020, 10(4), 135; https://doi.org/10.3390/metabo10040135 - 31 Mar 2020

Cited by 63 | Viewed by 11728

Abstract

Metabolomics analysis generates vast arrays of data, necessitating comprehensive workflows involving expertise in analytics, biochemistry and bioinformatics in order to provide coherent and high-quality data that enable discovery of robust and biologically significant metabolic findings. In this protocol article, we introduce notame, an analytical workflow for non-targeted metabolic profiling approaches, utilizing liquid chromatography–mass spectrometry analysis. We provide an overview of lab protocols and statistical methods that we commonly practice for the analysis of nutritional metabolomics data. The paper is divided into three main sections: the first and second sections introducing the background and the study designs available for metabolomics research and the third section describing in detail the steps of the main methods and protocols used to produce, preprocess and statistically analyze metabolomics data and, finally, to identify and interpret the compounds that have emerged as interesting. Full article

(This article belongs to the Special Issue Metabolomics Data Processing and Data Analysis—Current Best Practices)

► Show Figures

Graphical abstract

16 pages, 3543 KiB

Open AccessEditor’s ChoiceReview

Antifungal Drugs

by Jiří Houšť, Jaroslav Spížek and Vladimír Havlíček

Metabolites 2020, 10(3), 106; https://doi.org/10.3390/metabo10030106 - 12 Mar 2020

Cited by 136 | Viewed by 17216

Abstract

We reviewed the licensed antifungal drugs and summarized their mechanisms of action, pharmacological profiles, and susceptibility to specific fungi. Approved antimycotics inhibit 1,3-β-d-glucan synthase, lanosterol 14-α-demethylase, protein, and deoxyribonucleic acid biosynthesis, or sequestrate ergosterol. Their most severe side effects are hepatotoxicity, nephrotoxicity, and myelotoxicity. Whereas triazoles exhibit the most significant drug–drug interactions, echinocandins exhibit almost none. The antifungal resistance may be developed across most pathogens and includes drug target overexpression, efflux pump activation, and amino acid substitution. The experimental antifungal drugs in clinical trials are also reviewed. Siderophores in the Trojan horse approach or the application of siderophore biosynthesis enzyme inhibitors represent the most promising emerging antifungal therapies. Full article

(This article belongs to the Section Microbiology and Ecological Metabolomics)

► Show Figures

Graphical abstract

17 pages, 665 KiB

Open AccessEditor’s ChoiceReview

Important Considerations for Sample Collection in Metabolomics Studies with a Special Focus on Applications to Liver Functions

by Lorraine Smith, Joran Villaret-Cazadamont, Sandrine P. Claus, Cécile Canlet, Hervé Guillou, Nicolas J. Cabaton and Sandrine Ellero-Simatos

Metabolites 2020, 10(3), 104; https://doi.org/10.3390/metabo10030104 - 12 Mar 2020

Cited by 56 | Viewed by 5700

Abstract

Metabolomics has found numerous applications in the study of liver metabolism in health and disease. Metabolomics studies can be conducted in a variety of biological matrices ranging from easily accessible biofluids such as urine, blood or feces, to organs, tissues or even cells. Sample collection and storage are critical steps for which standard operating procedures must be followed. Inappropriate sample collection or storage can indeed result in high variability, interferences with instrumentation or degradation of metabolites. In this review, we will first highlight important general factors that should be considered when planning sample collection in the study design of metabolomic studies, such as nutritional status and circadian rhythm. Then, we will discuss in more detail the specific procedures that have been described for optimal pre-analytical handling of the most commonly used matrices (urine, blood, feces, tissues and cells). Full article

(This article belongs to the Special Issue Metabolism and Metabolomics of Liver in Health and Disease)

► Show Figures

Figure 1

23 pages, 1227 KiB

Open AccessEditor’s ChoiceReview

Metabolomics as an Emerging Tool for the Study of Plant–Pathogen Interactions

by Fernanda R. Castro-Moretti, Irene N. Gentzel, David Mackey and Ana P. Alonso

Metabolites 2020, 10(2), 52; https://doi.org/10.3390/metabo10020052 - 29 Jan 2020

Cited by 124 | Viewed by 11460

Abstract

Plants defend themselves from most microbial attacks via mechanisms including cell wall fortification, production of antimicrobial compounds, and generation of reactive oxygen species. Successful pathogens overcome these host defenses, as well as obtain nutrients from the host. Perturbations of plant metabolism play a central role in determining the outcome of attempted infections. Metabolomic analyses, for example between healthy, newly infected and diseased or resistant plants, have the potential to reveal perturbations to signaling or output pathways with key roles in determining the outcome of a plant–microbe interaction. However, application of this -omic and its tools in plant pathology studies is lagging relative to genomic and transcriptomic methods. Thus, it is imperative to bring the power of metabolomics to bear on the study of plant resistance/susceptibility. This review discusses metabolomics studies that link changes in primary or specialized metabolism to the defense responses of plants against bacterial, fungal, nematode, and viral pathogens. Also examined are cases where metabolomics unveils virulence mechanisms used by pathogens. Finally, how integrating metabolomics with other -omics can advance plant pathology research is discussed. Full article

(This article belongs to the Special Issue Metabolomic and Flux Analysis in Plants)

► Show Figures

Graphical abstract

23 pages, 2128 KiB

Open AccessEditor’s ChoiceReview

Salivary Metabolomics: From Diagnostic Biomarker Discovery to Investigating Biological Function

by Alexander Gardner, Guy Carpenter and Po-Wah So

Metabolites 2020, 10(2), 47; https://doi.org/10.3390/metabo10020047 - 26 Jan 2020

Cited by 84 | Viewed by 8145

Abstract

Metabolomic profiling of biofluids, e.g., urine, plasma, has generated vast and ever-increasing amounts of knowledge over the last few decades. Paradoxically, metabolomic analysis of saliva, the most readily-available human biofluid, has lagged. This review explores the history of saliva-based metabolomics and summarizes current knowledge of salivary metabolomics. Current applications of salivary metabolomics have largely focused on diagnostic biomarker discovery and the diagnostic value of the current literature base is explored. There is also a small, albeit promising, literature base concerning the use of salivary metabolomics in monitoring athletic performance. Functional roles of salivary metabolites remain largely unexplored. Areas of emerging knowledge include the role of oral host–microbiome interactions in shaping the salivary metabolite profile and the potential roles of salivary metabolites in oral physiology, e.g., in taste perception. Discussion of future research directions describes the need to begin acquiring a greater knowledge of the function of salivary metabolites, a current research direction in the field of the gut metabolome. The role of saliva as an easily obtainable, information-rich fluid that could complement other gastrointestinal fluids in the exploration of the gut metabolome is emphasized. Full article

(This article belongs to the Special Issue Metabolomics in Human Tissues and Materials)

► Show Figures

Figure 1

30 pages, 917 KiB

Open AccessEditor’s ChoiceReview

Metabolomics in the Context of Plant Natural Products Research: From Sample Preparation to Metabolite Analysis

by Mohamed A. Salem, Leonardo Perez de Souza, Ahmed Serag, Alisdair R. Fernie, Mohamed A. Farag, Shahira M. Ezzat and Saleh Alseekh

Metabolites 2020, 10(1), 37; https://doi.org/10.3390/metabo10010037 - 15 Jan 2020

Cited by 161 | Viewed by 13792

Abstract

Plant-derived natural products have long been considered a valuable source of lead compounds for drug development. Natural extracts are usually composed of hundreds to thousands of metabolites, whereby the bioactivity of natural extracts can be represented by synergism between several metabolites. However, isolating every single compound from a natural extract is not always possible due to the complex chemistry and presence of most secondary metabolites at very low levels. Metabolomics has emerged in recent years as an indispensable tool for the analysis of thousands of metabolites from crude natural extracts, leading to a paradigm shift in natural products drug research. Analytical methods such as mass spectrometry (MS) and nuclear magnetic resonance (NMR) are used to comprehensively annotate the constituents of plant natural products for screening, drug discovery as well as for quality control purposes such as those required for phytomedicine. In this review, the current advancements in plant sample preparation, sample measurements, and data analysis are presented alongside a few case studies of the successful applications of these processes in plant natural product drug discovery. Full article

(This article belongs to the Special Issue Sample Preparation in Metabolomics)

► Show Figures

Figure 1

Show export options Show export options

Select all

Export citation of selected articles as:

Displaying article 151-156 on page 4 of 4.

Go to page 2 3 4

Journal Menu

Journal Browser

Editor’s Choice Articles

Further Information

Guidelines

MDPI Initiatives

Follow MDPI