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Metabolites
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Metabolomics 2021 Online
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Metabolomics 2021 Online

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

Deadline for manuscript submissions: closed (1 December 2021) | Viewed by 19562

Special Issue Editors

Dr. Krista Zanetti

E-Mail Website
Guest Editor
National Cancer Institute, Rockville, MD 20850, USA
Interests: metabolomics; epidemiology; omics data integration
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Horst Joachim Schirra

E-Mail Website
Guest Editor
School of Environment and Science, and Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
Interests: NMR spectroscopy; metabolomics; C. elegans; genome-scale models; metabolic regulation; gasotransmitters; mitochondrial metabolism; hypometabolism; environmental metabolomics; foodomicsh

Special Issue Information

Dear Colleagues,

This Special Issue of Metabolites is the conference issue dedicated to Metabolomics 2021 Online.

For this Special Issue, we particularly, but not exclusively, welcome papers presented at or resulting from Metabolomics 2021 Online, the second virtual conference of the Metabolomics Society that took place from 22–24 June 2021. The focus of this issue is topics relevant to metabolomic science.

More information about the Metabolomics 2021 Online conference can be found at: https://metabolomics2021.org/.

We look forward to reading your papers! 

Dr. Krista Zanetti
Prof. 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.

Published Papers (6 papers)

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Research

14 pages, 1332 KiB  
Article
Asparagine Metabolism in Tumors Is Linked to Poor Survival in Females with Colorectal Cancer: A Cohort Study
by Xinyi Shen, Yuping Cai, Lingeng Lu, Huang Huang, Hong Yan, Philip B. Paty, Engjel Muca, Nita Ahuja, Yawei Zhang, Caroline H. Johnson and Sajid A. Khan
Metabolites 2022, 12(2), 164; https://doi.org/10.3390/metabo12020164 - 09 Feb 2022
Cited by 6 | Viewed by 2625
Abstract
The interplay between the sex-specific differences in tumor metabolome and colorectal cancer (CRC) prognosis has never been studied and represents an opportunity to improve patient outcomes. This study examines the link between tumor metabolome and prognosis by sex for CRC patients. Using untargeted [...] Read more.
The interplay between the sex-specific differences in tumor metabolome and colorectal cancer (CRC) prognosis has never been studied and represents an opportunity to improve patient outcomes. This study examines the link between tumor metabolome and prognosis by sex for CRC patients. Using untargeted metabolomics analysis, abundances of 91 metabolites were obtained from primary tumor tissues from 197 patients (N = 95 females, N = 102 males) after surgical colectomy for stage I-III CRC. Cox Proportional hazard (PH) regression models estimated the associations between tumor metabolome and 5-year overall survival (OS) and recurrence-free survival (RFS), and their interactions with sex. Eleven metabolites had significant sex differences in their associations with 5-year OS, and five metabolites for 5-year RFS. The metabolites asparagine and serine had sex interactions for both OS and RFS. Furthermore, in the asparagine synthetase (ASNS)-catalyzed asparagine synthesis pathway, asparagine was associated with substantially poorer OS (HR (95% CI): 6.39 (1.78–22.91)) and RFS (HR (95% CI): 4.36 (1.39–13.68)) for female patients only. Similar prognostic disadvantages in females were seen in lysophospholipid and polyamine synthesis. Unique metabolite profiles indicated that increased asparagine synthesis was associated with poorer prognosis for females only, providing insight into precision medicine for CRC treatment stratified by sex. Full article
(This article belongs to the Special Issue Metabolomics 2021 Online)
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18 pages, 5616 KiB  
Article
Identification and Distribution of Sterols, Bile Acids, and Acylcarnitines by LC–MS/MS in Humans, Mice, and Pigs—A Qualitative Analysis
by Ambrin Farizah Babu, Ville Mikael Koistinen, Soile Turunen, Gloria Solano-Aguilar, Joseph F. Urban, Jr., Iman Zarei and Kati Hanhineva
Metabolites 2022, 12(1), 49; https://doi.org/10.3390/metabo12010049 - 07 Jan 2022
Cited by 7 | Viewed by 3602
Abstract
Sterols, bile acids, and acylcarnitines are key players in human metabolism. Precise annotations of these metabolites with mass spectrometry analytics are challenging because of the presence of several isomers and stereoisomers, variability in ionization, and their relatively low concentrations in biological samples. Herein, [...] Read more.
Sterols, bile acids, and acylcarnitines are key players in human metabolism. Precise annotations of these metabolites with mass spectrometry analytics are challenging because of the presence of several isomers and stereoisomers, variability in ionization, and their relatively low concentrations in biological samples. Herein, we present a sensitive and simple qualitative LC–MS/MS (liquid chromatography with tandem mass spectrometry) method by utilizing a set of pure chemical standards to facilitate the identification and distribution of sterols, bile acids, and acylcarnitines in biological samples including human stool and plasma; mouse ileum, cecum, jejunum content, duodenum content, and liver; and pig bile, proximal colon, cecum, heart, stool, and liver. With this method, we detected 24 sterol, 32 bile acid, and 27 acylcarnitine standards in one analysis that were separated within 13 min by reversed-phase chromatography. Further, we observed different sterol, bile acid, and acylcarnitine profiles for the different biological samples across the different species. The simultaneous detection and annotation of sterols, bile acids, and acylcarnitines from reference standards and biological samples with high precision represents a valuable tool for screening these metabolites in routine scientific research. Full article
(This article belongs to the Special Issue Metabolomics 2021 Online)
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22 pages, 4020 KiB  
Article
A Metabolomic Study of Epichloë Endophytes for Screening Antifungal Metabolites
by Krishni Fernando, Priyanka Reddy, Kathryn M. Guthridge, German C. Spangenberg and Simone J. Rochfort
Metabolites 2022, 12(1), 37; https://doi.org/10.3390/metabo12010037 - 04 Jan 2022
Cited by 5 | Viewed by 2236
Abstract
Epichloë endophytes, fungal endosymbionts of Pooidae grasses, are commonly utilized in forage and turf industries because they produce beneficial metabolites that enhance resistance against environmental stressors such as insect feeding and disease caused by phytopathogen infection. In pastoral agriculture, phytopathogenic diseases impact both [...] Read more.
Epichloë endophytes, fungal endosymbionts of Pooidae grasses, are commonly utilized in forage and turf industries because they produce beneficial metabolites that enhance resistance against environmental stressors such as insect feeding and disease caused by phytopathogen infection. In pastoral agriculture, phytopathogenic diseases impact both pasture quality and animal production. Recently, bioactive endophyte strains have been reported to secrete compounds that significantly inhibit the growth of phytopathogenic fungi in vitro. A screen of previously described Epichloë-produced antifeedant and toxic alkaloids determined that the antifungal bioactivity observed is not due to the production of these known metabolites, and so there is a need for methods to identify new bioactive metabolites. The process described here is applicable more generally for the identification of antifungals in new endophytes. This study aims to characterize the fungicidal potential of novel, ‘animal friendly’ Epichloë endophyte strains NEA12 and NEA23 that exhibit strong antifungal activity using an in vitro assay. Bioassay-guided fractionation, followed by metabolite analysis, identified 61 metabolites that, either singly or in combination, are responsible for the observed bioactivity. Analysis of the perennial ryegrass-endophyte symbiota confirmed that NEA12 and NEA23 produce the prospective antifungal metabolites in symbiotic association and thus are candidates for compounds that promote disease resistance in planta. The “known unknown” suite of antifungal metabolites identified in this study are potential biomarkers for the selection of strains that enhance pasture and turf production through better disease control. Full article
(This article belongs to the Special Issue Metabolomics 2021 Online)
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14 pages, 1030 KiB  
Article
Plasma Metabolomic Profiles Associated with Three-Year Progression of Age-Related Macular Degeneration
by Ines Lains, Kevin Mendez, Archana Nigalye, Raviv Katz, Vivian Paraskevi Douglas, Rachel S. Kelly, Ivana K. Kim, John B. Miller, Demetrios G. Vavvas, Liming Liang, Jessica Lasky-Su, Joan W. Miller and Deeba Husain
Metabolites 2022, 12(1), 32; https://doi.org/10.3390/metabo12010032 - 01 Jan 2022
Cited by 7 | Viewed by 2347
Abstract
Plasma metabolomic profiles have been shown to be associated with age-related macular degeneration (AMD) and its severity stages. However, all studies performed to date have been cross-sectional and have not assessed progression of AMD. This prospective, longitudinal, pilot study analyzes, for the first [...] Read more.
Plasma metabolomic profiles have been shown to be associated with age-related macular degeneration (AMD) and its severity stages. However, all studies performed to date have been cross-sectional and have not assessed progression of AMD. This prospective, longitudinal, pilot study analyzes, for the first time, the association between plasma metabolomic profiles and progression of AMD over a 3-year period. At baseline and 3 years later, subjects with AMD (n = 108 eyes) and controls (n = 45 eyes) were imaged with color fundus photos for AMD staging and tested for retinal function with dark adaptation (DA). Fasting plasma samples were also collected for metabolomic profiling. AMD progression was considered present if AMD stage at 3 years was more advanced than at baseline (n = 26 eyes, 17%). Results showed that, of the metabolites measured at baseline, eight were associated with 3-year AMD progression (p < 0.01) and 19 (p < 0.01) with changes in DA. Additionally, changes in the levels (i.e., between 3 years and baseline) of 6 and 17 metabolites demonstrated significant associations (p < 0.01) with AMD progression and DA, respectively. In conclusion, plasma metabolomic profiles are associated with clinical and functional progression of AMD at 3 years. These findings contribute to our understanding of mechanisms of AMD progression and the identification of potential therapeutics for this blinding disease. Full article
(This article belongs to the Special Issue Metabolomics 2021 Online)
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14 pages, 2637 KiB  
Article
Methodology for Single Bee and Bee Brain 1H-NMR Metabolomics
by Jayne C. McDevitt, Riju A. Gupta, Sydney G. Dickinson, Phillip L. Martin, Jean Rieuthavorn, Amy Freund, Marie C. Pizzorno, Elizabeth A. Capaldi and David Rovnyak
Metabolites 2021, 11(12), 864; https://doi.org/10.3390/metabo11120864 - 13 Dec 2021
Cited by 1 | Viewed by 3313
Abstract
The feasibility of metabolomic 1H NMR spectroscopy is demonstrated for its potential to help unravel the complex factors that are impacting honeybee health and behavior. Targeted and non-targeted 1H NMR metabolic profiles of liquid and tissue samples of organisms could provide [...] Read more.
The feasibility of metabolomic 1H NMR spectroscopy is demonstrated for its potential to help unravel the complex factors that are impacting honeybee health and behavior. Targeted and non-targeted 1H NMR metabolic profiles of liquid and tissue samples of organisms could provide information on the pathology of infections and on environmentally induced stresses. This work reports on establishing extraction methods for NMR metabolic characterization of Apis mellifera, the European honeybee, describes the currently assignable aqueous metabolome, and gives examples of diverse samples (brain, head, body, whole bee) and biologically meaningful metabolic variation (drone, forager, day old, deformed wing virus). Both high-field (600 MHz) and low-field (80 MHz) methods are applicable, and 1H NMR can observe a useful subset of the metabolome of single bees using accessible NMR instrumentation (600 MHz, inverse room temperature probe) in order to avoid pooling several bees. Metabolite levels and changes can be measured by NMR in the bee brain, where dysregulation of metabolic processes has been implicated in colony collapse. For a targeted study, the ability to recover 10-hydroxy-2-decenoic acid in mandibular glands is shown, as well as markers of interest in the bee brain such as GABA (4-aminobutyrate), proline, and arginine. The findings here support the growing use of 1H NMR more broadly in bees, native pollinators, and insects. Full article
(This article belongs to the Special Issue Metabolomics 2021 Online)
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15 pages, 2987 KiB  
Article
Metabolomic Changes in Naturally MAP-Infected Holstein–Friesian Heifers Indicate Immunologically Related Biochemical Reprogramming
by Emma N. Taylor, Manfred Beckmann, Bernardo Villarreal-Ramos, Hans-Martin Vordermeier, Glyn Hewinson, David Rooke, Luis A. J. Mur and Ad P. Koets
Metabolites 2021, 11(11), 727; https://doi.org/10.3390/metabo11110727 - 23 Oct 2021
Cited by 6 | Viewed by 2652
Abstract
Johne’s disease, caused by Mycobacterium avium subsp. paratuberculosis (MAP), causes weight loss, diarrhoea, and reduced milk yields in clinically infected cattle. Asymptomatic, subclinically infected cattle shed MAP bacteria but are frequently not detected by diagnostic tests. Herein, we compare the metabolite profiles of [...] Read more.
Johne’s disease, caused by Mycobacterium avium subsp. paratuberculosis (MAP), causes weight loss, diarrhoea, and reduced milk yields in clinically infected cattle. Asymptomatic, subclinically infected cattle shed MAP bacteria but are frequently not detected by diagnostic tests. Herein, we compare the metabolite profiles of sera from subclinically infected Holstein–Friesian heifers and antibody binding to selected MAP antigens. The study used biobanked serum samples from 10 naturally MAP-infected and 10 control heifers, sampled monthly from ~1 to 19 months of age. Sera were assessed using flow infusion electrospray–high-resolution mass spectrometry (FIE–HRMS) on a Q Exactive hybrid quadrupole–Orbitrap mass spectrometer for high-throughput, sensitive, non-targeted metabolite fingerprinting. Partial least-squares discriminant analyses (PLS-DA) and hierarchical cluster analysis (HCA) of the data discriminated between naturally MAP-infected and control heifers. In total, 33 metabolites that differentially accumulated in naturally MAP-infected heifers compared to controls were identified. Five were significantly elevated within MAP-infected heifers throughout the study, i.e., leukotriene B4, bicyclo prostaglandin E2 (bicyclo PGE2), itaconic acid, 2-hydroxyglutaric acid and N6-acetyl-L-lysine. These findings highlight the potential of metabolomics in the identification of novel MAP diagnostic markers and particular biochemical pathways, which may provide insights into the bovine immune response to MAP. Full article
(This article belongs to the Special Issue Metabolomics 2021 Online)
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