Special Issue "NMR-based Metabolomics and Its Applications Volume 2"

A special issue of Metabolites (ISSN 2218-1989).

Deadline for manuscript submissions: 31 May 2019

Special Issue Editors

Guest Editor
Dr. Flaminia Cesare Marincola

Università di Cagliari
Website | E-Mail
Phone: +39 070 675 4389
Interests: NMR spectroscopy; metabolomics; food analysis; infant metabolism
Guest Editor
Prof. Luisa Mannina

Sapienza University of Rome
Website | E-Mail
Interests: NMR spectroscopy; metabolomics; food chemistry

Special Issue Information

Dear Colleagues,

Over the last decade, the number of scientific publications in the metabolomics area has increased exponentially. The literature analysis included ca 23,000 articles during the period 2008 to 2017, revealing metabolomics applications in a wide range of fields including medical, plant, animal, and food sciences (this bibliographic data was retrieved from the SCOPUS database searching “metabolomics” in article abstract, title, and keywords). The high applicability of this approach is due to its ability to qualitatively and quantitatively characterize the chemical profile of all the low molecular weight metabolites (metabolome) present in cells, tissues, organs, and biological fluids as end products of the cellular regulatory pathways. Thus, providing a snapshot of the phenotype of a biological system, metabolomics offers useful contributions to a comprehensive insight into the functional status of human, animal, plant, and microbe organisms.

The main analytical platforms employed in metabolomics are Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry (MS). Both methods have advantages and limitations. They are often used separately, although their combination can help overcome the respective limitations, providing a more comprehensive insight into important metabolic processes.

This Special Issue is focused on the recent technical advances and practical applications of NMR spectroscopy to metabolomics analyses. Submissions of both original research and review articles are welcomed. Topics of this Special Issue include, but are not limited to:

  • Biomedical research
  • Clinical toxicolology
  • Pharmacology
  • Drug discovery
  • Food science
  • Nutrition research
  • Herbal medicines
  • Microbiology
  • Marine biology
  • Environmental sciences
  • Aquaculture
  • Sport and exercise science

Dr. Flaminia Cesare Marincola
Prof. Dr. Luisa Mannina
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 papers will be 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 1000 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

  • metabolomics
  • NMR
  • clinical application
  • food and nutritional science 
  • microbiology
  • marine biology
  • environmental science
  • sport and exercise science

Published Papers (10 papers)

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Research

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Open AccessArticle
NMR-Based Tissular and Developmental Metabolomics of Tomato Fruit
Metabolites 2019, 9(5), 93; https://doi.org/10.3390/metabo9050093
Received: 11 April 2019 / Revised: 30 April 2019 / Accepted: 7 May 2019 / Published: 9 May 2019
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Abstract
Fruit is a complex organ containing seeds and several interconnected tissues with dedicated roles. However, most biochemical or molecular studies about fleshy fruit development concern the entire fruit, the fruit without seeds, or pericarp only. We studied tomato (Solanum lycopersicum) fruit [...] Read more.
Fruit is a complex organ containing seeds and several interconnected tissues with dedicated roles. However, most biochemical or molecular studies about fleshy fruit development concern the entire fruit, the fruit without seeds, or pericarp only. We studied tomato (Solanum lycopersicum) fruit at four stages of development (12, 20, 35, and 45 days post-anthesis). We separated the seeds and the other tissues, exocarp, mesocarp, columella with placenta and locular tissue, and analyzed them individually using proton NMR metabolomic profiling for the quantification of major polar metabolites, enzymatic analysis of starch, and LC-DAD analysis of isoprenoids. Pericarp tissue represented about half of the entire fruit mass only. The composition of each fruit tissue changed during fruit development. An ANOVA-PCA highlighted common, and specific metabolite trends between tissues e.g., higher contents of chlorogenate in locular tissue and of starch in columella. Euclidian distances based on compositional data showed proximities within and between tissues. Several metabolic regulations differed between tissues as revealed by the comparison of metabolite networks based on correlations between compounds. This work stressed the role of specific tissues less studied than pericarp but that impact fruit organoleptic quality including its shape and taste, and fruit processing quality. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Applications Volume 2)
Open AccessArticle
Extra-Virgin Olive Oils from Nine Italian Regions: An 1H NMR-Chemometric Characterization
Metabolites 2019, 9(4), 65; https://doi.org/10.3390/metabo9040065
Received: 18 February 2019 / Revised: 29 March 2019 / Accepted: 29 March 2019 / Published: 3 April 2019
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Abstract
Extra-virgin olive oil (383 samples; EVOOs) of three consecutive harvesting years from nine Italian regions were collected and submitted to an 1H NMR-chemometric protocol to characterize the samples according to their origin (geographical area and variety). A more complete assignment of the [...] Read more.
Extra-virgin olive oil (383 samples; EVOOs) of three consecutive harvesting years from nine Italian regions were collected and submitted to an 1H NMR-chemometric protocol to characterize the samples according to their origin (geographical area and variety). A more complete assignment of the olive oil 1H spectrum in CDCl3 and DMSOd6 was reported identifying 24-methylencycolartanol. A single classification model provided the discrimination of EVOOs among the three geographical macro-areas (North, Islands, Center-South), whereas a hierarchical approach based on breaking the overall classification problem into a series of smaller linear discriminant analysis (LDA) sub-models was tested to differentiate olive oils according to their geographical regions. Specific compounds responsible for olive oil characterization were identified. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Applications Volume 2)
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Open AccessArticle
Characterization of Yak Common Biofluids Metabolome by Means of Proton Nuclear Magnetic Resonance Spectroscopy
Metabolites 2019, 9(3), 41; https://doi.org/10.3390/metabo9030041
Received: 14 February 2019 / Accepted: 25 February 2019 / Published: 2 March 2019
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Abstract
The aim of this study was to evaluate the metabolic profiles of yak (Bos grunniens) serum, feces, and urine by using proton nuclear magnetic resonance (1H-NMR), to serve as a reference guide for the healthy yak milieu. A total [...] Read more.
The aim of this study was to evaluate the metabolic profiles of yak (Bos grunniens) serum, feces, and urine by using proton nuclear magnetic resonance (1H-NMR), to serve as a reference guide for the healthy yak milieu. A total of 108 metabolites, giving information about diet, protein digestion, and energy generation or gut-microbial co-metabolism, were assigned across the three biological matrices. A core metabolome of 15 metabolites was ubiquitous across all biofluids. Lactate, acetate, and creatinine could be regarded as the most abundant metabolites in the metabolome of serum, feces, and urine, respectively. Metabolic pathway analysis showed that the molecules identified could be able to give thorough information about four main metabolic pathways, namely valine, leucine, and isoleucine biosynthesis; phenylalanine, tyrosine, and tryptophan biosynthesis; glutamine and glutamate metabolism; and taurine and hypotaurine metabolism. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Applications Volume 2)
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Open AccessArticle
NMR Metabolomic Analysis of Skeletal Muscle, Heart, and Liver of Hatchling Loggerhead Sea Turtles (Caretta caretta) Experimentally Exposed to Crude Oil and/or Corexit
Metabolites 2019, 9(2), 21; https://doi.org/10.3390/metabo9020021
Received: 21 December 2018 / Revised: 20 January 2019 / Accepted: 23 January 2019 / Published: 26 January 2019
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Abstract
We used nuclear magnetic spectroscopy (NMR) to evaluate the metabolic impacts of crude oil, Corexit 5900A, a dispersant, and a crude oil Corexit 5900A mixture exposure on skeletal muscle, heart, and liver physiology of hatchling loggerhead sea turtles (Caretta caretta). Tissue [...] Read more.
We used nuclear magnetic spectroscopy (NMR) to evaluate the metabolic impacts of crude oil, Corexit 5900A, a dispersant, and a crude oil Corexit 5900A mixture exposure on skeletal muscle, heart, and liver physiology of hatchling loggerhead sea turtles (Caretta caretta). Tissue samples were obtained from 22 seven-day-old hatchlings after a four day cutaneous exposure to environmentally relevant concentrations of crude oil, Corexit 5900A, a combination of crude oil and Corexit 9500A, or a seawater control. We identified 38 metabolites in the aqueous extracts of the liver, and 30 metabolites in both the skeletal and heart muscle aqueous extracts, including organic acids/osmolytes, energy compounds, amino acids, ketone bodies, nucleosides, and nucleotides. Skeletal muscle lactate, creatines, and taurine concentrations were significantly lower in hatchlings exposed to crude oil than in control hatchlings. Lactate, taurine, and cholines appeared to be the basis of some variation in hatchling heart samples, and liver inosine, uracil, and uridine appeared to be influenced by Corexit and crude oil exposure. Observed decreases in concentrations of lactate and creatines may reflect energy depletion in skeletal muscle of oil-exposed animals, while decreased taurine concentrations in these animals may reflect higher oxidative stress. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Applications Volume 2)
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Open AccessArticle
Univariate Statistical Analysis as a Guide to 1H-NMR Spectra Signal Assignment by Visual Inspection
Metabolites 2019, 9(1), 15; https://doi.org/10.3390/metabo9010015
Received: 20 December 2018 / Revised: 8 January 2019 / Accepted: 10 January 2019 / Published: 15 January 2019
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Abstract
In Proton Nuclear Magnetic Resonance (1H-NMR) spectroscopy, the signals assignment procedure is normally conducted by visual inspection of the spectra, by taking advantage of the innate predisposition of human eye for pattern recognition. In the case of untargeted metabolomics investigations on [...] Read more.
In Proton Nuclear Magnetic Resonance (1H-NMR) spectroscopy, the signals assignment procedure is normally conducted by visual inspection of the spectra, by taking advantage of the innate predisposition of human eye for pattern recognition. In the case of untargeted metabolomics investigations on food and body fluids, the complexity of the spectra may lead the user to overlook signals, independently from their biological relevance. Here, we describe a four steps procedure that is designed to guide signals assignment task by visual inspection. The procedure can be employed whenever an experimental plan allows for the application of a univariate statistical analysis on a point-by-point basis, which is commonly the case. By comparing, as a proof of concept, 1H-NMR spectra of vaginal fluids of healthy and bacterial vaginosis (BV) affected women, we show that the procedure is also readily usable by non-experts in three particularly challenging cases: overlapping multiplets, poorly aligned signals, and signals with very poor signal-to-noise ratio. The paper is accompanied by the necessary codes and examples written in R computational language to allow the interested user gaining a hands-on impression of the procedure’s strengths and weaknesses. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Applications Volume 2)
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Open AccessArticle
Rapid Cerebral Metabolic Shift during Neonatal Sepsis Is Attenuated by Enteral Colostrum Supplementation in Preterm Pigs
Metabolites 2019, 9(1), 13; https://doi.org/10.3390/metabo9010013
Received: 3 December 2018 / Revised: 4 January 2019 / Accepted: 7 January 2019 / Published: 11 January 2019
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Abstract
Sepsis, the clinical manifestation of serious infection, may disturb normal brain development, especially in preterm infants with an immature brain. We hypothesized that neonatal sepsis induces systemic metabolic alterations that rapidly affect metabolic signatures in immature brain and cerebrospinal fluid (CSF). Cesarean-delivered preterm [...] Read more.
Sepsis, the clinical manifestation of serious infection, may disturb normal brain development, especially in preterm infants with an immature brain. We hypothesized that neonatal sepsis induces systemic metabolic alterations that rapidly affect metabolic signatures in immature brain and cerebrospinal fluid (CSF). Cesarean-delivered preterm pigs systemically received 109 CFU/kg Staphylococcus epidermidis (SE) and were provided total parenteral nutrition (n = 9) or enteral supplementation with bovine colostrum (n = 10) and compared with uninfected pigs receiving parenteral nutrition (n = 7). Plasma, CSF, and brain tissue samples were collected after 24 h and analyzed by 1H NMR-based metabolomics. Both plasma and CSF metabolomes revealed SE-induced changes in metabolite levels that reflected a modified energy metabolism. Hence, increased plasma lactate, alanine, and succinate levels, as well as CSF lactate levels, were observed during SE infection (all p < 0.05, ANOVA analysis). Myo-inositol, a glucose derivative known for beneficial effects on lung maturation in preterm infants, was also increased in plasma and CSF following SE infection. Enteral colostrum supplementation attenuated the lactate accumulation in blood and CSF. Bloodstream infection in preterm newborns was found to induce a rapid metabolic shift in both plasma and CSF, which was modulated by colostrum feeding. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Applications Volume 2)
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Open AccessArticle
Metabolomics of Breast Milk: The Importance of Phenotypes
Metabolites 2018, 8(4), 79; https://doi.org/10.3390/metabo8040079
Received: 25 October 2018 / Revised: 15 November 2018 / Accepted: 17 November 2018 / Published: 20 November 2018
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Abstract
Breast milk is the gold standard of nutrition for newborns. Its composition is tailored to the nutritional needs of the infant and varies between mothers. In recent years, several bioactive molecules have been discovered in addition to the main nutrients, such as multipotent [...] Read more.
Breast milk is the gold standard of nutrition for newborns. Its composition is tailored to the nutritional needs of the infant and varies between mothers. In recent years, several bioactive molecules have been discovered in addition to the main nutrients, such as multipotent stem cells, hormones, immunoglobulins, and bacteria. Furthermore, the human milk oligosaccharides (HMOs) seem to exert several important protective biological functions. According to the HMOs’ composition, breast milk can be classified as a secretory or non-secretory phenotype. In our study, we investigated the metabolome of milk collected from 58 mothers that delivered neonates at term, that were appropriate, small or large for gestational age, by performing nuclear magnetic resonance spectroscopy (1H-NMR). From the data analysis, two groups were distinguished based on their different types of oligosaccharides, and classified according the mother phenotype: secretory and non-secretory. This information is of major importance given the different biological function of the different HMOs, such as immune-modulation and protection against disease. This would allow us to predict whether the neonate would be, for instance, more prone to developing certain diseases, and to tailor her or his nutrition to fit their needs perfectly and pave the way to a personalized nutrition. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Applications Volume 2)
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Open AccessArticle
Traceability of “Tuscan PGI” Extra Virgin Olive Oils by 1H NMR Metabolic Profiles Collection and Analysis
Metabolites 2018, 8(4), 60; https://doi.org/10.3390/metabo8040060
Received: 11 September 2018 / Revised: 26 September 2018 / Accepted: 28 September 2018 / Published: 30 September 2018
Cited by 2 | PDF Full-text (3437 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
According to Coldiretti, Italy still continues to hold the European Quality record in extra virgin olive oils with origin designation and protected geographical indication (PDO and PGI). To date, 46 Italian brands are recognized by the European Union: 42 PDO and 4 PGI [...] Read more.
According to Coldiretti, Italy still continues to hold the European Quality record in extra virgin olive oils with origin designation and protected geographical indication (PDO and PGI). To date, 46 Italian brands are recognized by the European Union: 42 PDO and 4 PGI (Tuscan PGI, Calabria PGI; Tuscia PGI and PGI Sicily). Specific regulations, introduced for these quality marks, include the designation of both the geographical areas and the plant varieties contributing to the composition of the olive oil. However, the PDO and PGI assessment procedures are currently based essentially on farmer declarations. Tuscan PGI extra virgin olive oil is one of the best known Italian trademarks around the world. Tuscan PGI varietal platform is rather wide including 31 specific olive cultivars which should account for at least 95% of the product. On the other hand, while the characteristics of other popular Italian extra virgin olive oils (EVOOs) cultivars from specific geographical areas have been extensively studied (such as those of Coratina based blends from Apulia), little is still known about Tuscan PGI EVOO constituents. In this work, we performed, for the first time, a large-scale analysis of Tuscan PGI monocultivar olive oils by 1H NMR spectroscopy and multivariate statistical analyses (MVA). After genetic characterization of 217 leaf samples from 24 selected geographical areas, distributed all over the Tuscany, a number of 202 micro-milled oil samples including 10 PGI cultivars, was studied. The results of the present work confirmed the need of monocultivar genetically certified EVOO samples for the construction of 1H-NMR-metabolic profiles databases suitable for cultivar and/or geographical origin assessment. Such specific PGI EVOOs databases could be profitably used to justify the high added value of the product and the sustainability of the related supply chain. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Applications Volume 2)
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Review

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Open AccessReview
Current Developments in µMAS NMR Analysis for Metabolomics
Metabolites 2019, 9(2), 29; https://doi.org/10.3390/metabo9020029
Received: 26 December 2018 / Revised: 2 February 2019 / Accepted: 4 February 2019 / Published: 6 February 2019
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Abstract
Analysis of microscopic specimens has emerged as a useful analytical application in metabolomics because of its capacity for characterizing a highly homogenous sample with a specific interest. The undeviating analysis helps to unfold the hidden activities in a bulk specimen and contributes to [...] Read more.
Analysis of microscopic specimens has emerged as a useful analytical application in metabolomics because of its capacity for characterizing a highly homogenous sample with a specific interest. The undeviating analysis helps to unfold the hidden activities in a bulk specimen and contributes to the understanding of the fundamental metabolisms in life. In NMR spectroscopy, micro(µ)-probe technology is well-established and -adopted to the microscopic level of biofluids. However, this is quite the contrary with specimens such as tissue, cell and organism. This is due to the substantial difficulty of developing a sufficient µ-size magic-angle spinning (MAS) probe for sub-milligram specimens with the capability of high-quality data acquisition. It was not until 2012; a µMAS probe had emerged and shown promises to µg analysis; since, a continuous advancement has been made striving for the possibility of µMAS to be an effective NMR spectroscopic analysis. Herein, the mini-review highlights the progress of µMAS development—from an impossible scenario to an attainable solution—and describes a few demonstrative metabolic profiling studies. The review will also discuss the current challenges in µMAS NMR analysis and its potential to metabolomics. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Applications Volume 2)
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Other

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Open AccessBrief Report
1D “Spikelet” Projections from Heteronuclear 2D NMR Data—Permitting 1D Chemometrics While Preserving 2D Dispersion
Metabolites 2019, 9(1), 16; https://doi.org/10.3390/metabo9010016
Received: 13 December 2018 / Revised: 8 January 2019 / Accepted: 9 January 2019 / Published: 16 January 2019
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Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for the non-targeted metabolomics of intact biofluids and even living organisms. However, spectral overlap can limit the information that can be obtained from 1D 1H NMR. For example, magnetic susceptibility broadening in living organisms [...] Read more.
Nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for the non-targeted metabolomics of intact biofluids and even living organisms. However, spectral overlap can limit the information that can be obtained from 1D 1H NMR. For example, magnetic susceptibility broadening in living organisms prevents any metabolic information being extracted from solution-state 1D 1H NMR. Conversely, the additional spectral dispersion afforded by 2D 1H-13C NMR allows a wide range of metabolites to be assigned in-vivo in 13C enriched organisms, as well as a greater depth of information for biofluids in general. As such, 2D 1H-13C NMR is becoming more and more popular for routine metabolic screening of very complex samples. Despite this, there are only a very limited number of statistical software packages that can handle 2D NMR datasets for chemometric analysis. In comparison, a wide range of commercial and free tools are available for analysis of 1D NMR datasets. Overtime, it is likely more software solutions will evolve that can handle 2D NMR directly. In the meantime, this application note offers a simple alternative solution that converts 2D 1H-13C Heteronuclear Single Quantum Correlation (HSQC) data into a 1D “spikelet” format that preserves not only the 2D spectral information, but also the 2D dispersion. The approach allows 2D NMR data to be converted into a standard 1D Bruker format that can be read by software packages that can only handle 1D NMR data. This application note uses data from Daphnia magna (water fleas) in-vivo to demonstrate how to generate and interpret the converted 1D spikelet data from 2D datasets, including the code to perform the conversion on Bruker spectrometers. Full article
(This article belongs to the Special Issue NMR-based Metabolomics and Its Applications Volume 2)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Author: Jeremy Nicholson
Affiliation: Imperial College London, UK

Author: Valérie Copié
Affiliation: Montana State University, USA

Authors: Giorgia Conta, Giorgio Capuani, Alberta Tomassini, Fabio Sciubba, Maria Enrica Di Cocco and Alfredo Miccheli
Affiliation: Department of Chemistry, Sapienza University of Rome, Italy
Tentative title: The evolution of infant gut microbiota during the breastfeeding and weaning as investigated by 1H NMR-based metabolomics: a mother-infant dyad case report

 

 


 

 

 

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