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Book ; Online: Research in Metabolomics via Nuclear Magnetic Resonance Spectroscopy: Data Mining, Biochemistry and Clinical Chemistry

Vignoli, Alessia / Meoni, Gaia / Tenori, Leonardo

2022

Keywords	Research & information: general ; Biology, life sciences ; Biochemistry ; NMR metabolomics ; human plasma ; COVID-19 ; exhaled breath condensate ; nanoparticles exposure ; metabolomics ; colorectal cancer ; nuclear magnetic resonance ; surgery ; relapse ; phenotyping ; nuclear magnetic resonance spectroscopy ; coffee beans ; coffee processing ; coffee varieties ; post-harvest treatment ; NMR spectroscopy ; neonatal sepsis ; EOS ; LOS ; preterm birth ; NMR ; biomarkers ; clustering ; artificial intelligence ; machine learning ; deep learning ; health science ; n/a
Language	0\|e
Size	1 electronic resource (136 pages)
Publisher	MDPI - Multidisciplinary Digital Publishing Institute
Publishing place	Basel
Document type	Book ; Online
Note	English ; Open Access
HBZ-ID	HT021613693
ISBN	9783036545547 ; 3036545549
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article ; Online: Applications and Challenges for Metabolomics via Nuclear Magnetic Resonance Spectroscopy

Alessia Vignoli / Gaia Meoni / Leonardo Tenori

Applied Sciences, Vol 12, Iss 4655, p

2022 Volume 4655

Abstract: Even though metabolomics is about 20 years old, the interest in this “-omic” science is still growing, and high expectations remain in the scientific community for new practical applications in biomedicine and in the agricultural field [.] ...

Abstract	Even though metabolomics is about 20 years old, the interest in this “-omic” science is still growing, and high expectations remain in the scientific community for new practical applications in biomedicine and in the agricultural field [.]
Keywords	n/a ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Nuclear Magnetic Resonance-Based Metabolomic Comparison of Breast Milk and Organic and Traditional Formula Milk Brands for Infants and Toddlers.

Meoni, Gaia / Tenori, Leonardo / Luchinat, Claudio

Omics : a journal of integrative biology

2020 Volume 24, Issue 7, Page(s) 424–436

Abstract: In recent years, new formula milk (FM) products based on milk from farms that strictly adhere to the "organic farming" practices became available. However, little is known about the differences in nutritional profile of these organic formulae with ... ...

Abstract	In recent years, new formula milk (FM) products based on milk from farms that strictly adhere to the "organic farming" practices became available. However, little is known about the differences in nutritional profile of these organic formulae with respect to traditional ones. We comprehensively evaluated the metabolite profiles of FM with nuclear magnetic resonance (NMR)-based metabolomic analysis. Five commercial brands of organic and nonorganic formula liquid milk for infants (0-12 months) and toddlers (1-3 years) were analyzed, together with human milk (HM) samples. Proton NMR (
MeSH term(s)	Child, Preschool ; Humans ; Infant ; Infant Formula/analysis ; Infant, Newborn ; Magnetic Resonance Spectroscopy/methods ; Metabolomics/methods ; Milk, Human/chemistry ; Reproducibility of Results ; Sensitivity and Specificity
Language	English
Publishing date	2020-06-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2030312-9
ISSN	1557-8100 ; 1536-2310
ISSN (online)	1557-8100
ISSN	1536-2310
DOI	10.1089/omi.2019.0125
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Article ; Online: Metabolomics profile in gastrointestinal cancers: Update and future perspectives.

Nannini, Giulia / Meoni, Gaia / Amedei, Amedeo / Tenori, Leonardo

World journal of gastroenterology

2020 Volume 26, Issue 20, Page(s) 2514–2532

Abstract: Despite recent progress in diagnosis and therapy, gastrointestinal (GI) cancers remain one of the most important causes of death with a poor prognosis due to late diagnosis. Serum tumor markers and detection of occult blood in the stool are the current ... ...

Abstract	Despite recent progress in diagnosis and therapy, gastrointestinal (GI) cancers remain one of the most important causes of death with a poor prognosis due to late diagnosis. Serum tumor markers and detection of occult blood in the stool are the current tests used in the clinic of GI cancers; however, these tests are not useful as diagnostic screening since they have low specificity and low sensitivity. Considering that one of the hallmarks of cancer is dysregulated metabolism and metabolomics is an optimal approach to illustrate the metabolic mechanisms that belong to living systems, is now clear that this -omics could open a new way to study cancer. In the last years, nuclear magnetic resonance (NMR) metabolomics has demonstrated to be an optimal approach for diseases' diagnosis nevertheless a few studies focus on the NMR capability to find new biomarkers for early diagnosis of GI cancers. For these reasons in this review, we will give an update on the status of NMR metabolomic studies for the diagnosis and development of GI cancers using biological fluids.
MeSH term(s)	Biomarkers, Tumor/analysis ; Biomarkers, Tumor/metabolism ; Early Detection of Cancer/methods ; Early Detection of Cancer/trends ; Feces/chemistry ; Gastrointestinal Neoplasms/blood ; Gastrointestinal Neoplasms/diagnosis ; Gastrointestinal Neoplasms/metabolism ; Gastrointestinal Neoplasms/urine ; Humans ; Magnetic Resonance Spectroscopy ; Metabolomics/methods ; Metabolomics/trends
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2020-06-09
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2185929-2
ISSN	2219-2840 ; 1007-9327
ISSN (online)	2219-2840
ISSN	1007-9327
DOI	10.3748/wjg.v26.i20.2514
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Article ; Online: Fingerprinting and profiling in metabolomics of biosamples.

Ghini, Veronica / Meoni, Gaia / Vignoli, Alessia / Di Cesare, Francesca / Tenori, Leonardo / Turano, Paola / Luchinat, Claudio

Progress in nuclear magnetic resonance spectroscopy

2023 Volume 138-139, Page(s) 105–135

Abstract: This review focuses on metabolomics from an NMR point of view. It attempts to cover the broad scope of metabolomics and describes the NMR experiments that are most suitable for each sample type. It is addressed not only to NMR specialists, but to all ... ...

Abstract	This review focuses on metabolomics from an NMR point of view. It attempts to cover the broad scope of metabolomics and describes the NMR experiments that are most suitable for each sample type. It is addressed not only to NMR specialists, but to all researchers who wish to approach metabolomics with a clear idea of what they wish to achieve but not necessarily with a deep knowledge of NMR. For this reason, some technical parts may seem a bit naïve to the experts. The review starts by describing standard metabolomics procedures, which imply the use of a dedicated 600 MHz instrument and of four properly standardized 1D experiments. Standardization is a must if one wants to directly compare NMR results obtained in different labs. A brief mention is also made of standardized pre-analytical procedures, which are even more essential. Attention is paid to the distinction between fingerprinting and profiling, and the advantages and disadvantages of fingerprinting are clarified. This aspect is often not fully appreciated. Then profiling, and the associated problems of signal assignment and quantitation, are discussed. We also describe less conventional approaches, such as the use of different magnetic fields, the use of signal enhancement techniques to increase sensitivity, and the potential of field-shuttling NMR. A few examples of biomedical applications are also given, again with the focus on NMR techniques that are most suitable to achieve each particular goal, including a description of the most common heteronuclear experiments. Finally, the growing applications of metabolomics to foodstuffs are described.
MeSH term(s)	Metabolomics/methods ; Magnetic Resonance Spectroscopy/methods
Language	English
Publishing date	2023-10-18
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	209325-x
ISSN	1873-3301 ; 0079-6565
ISSN (online)	1873-3301
ISSN	0079-6565
DOI	10.1016/j.pnmrs.2023.10.002
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Article ; Online: Phenotyping Green and Roasted Beans of Nicaraguan Coffea Arabica Varieties Processed with Different Post-Harvest Practices

Gaia Meoni / Claudio Luchinat / Enrico Gotti / Alejandro Cadena / Leonardo Tenori

Applied Sciences, Vol 11, Iss 11779, p

2021 Volume 11779

Abstract: Metabolomic tecniques have already been used to characterize two of the most common coffee species, C. arabica and C. canephora , but no studies have focused on the characterization of green and roasted coffee varieties of a certain species. We aim to ... ...

Abstract	Metabolomic tecniques have already been used to characterize two of the most common coffee species, C. arabica and C. canephora , but no studies have focused on the characterization of green and roasted coffee varieties of a certain species. We aim to provide, using NMR-based metabolomics, detailed and comprehensive information regarding the compositional differences of seven coffee varieties ( C. arabica ) of green and roasted coffee bean batches from Nicaragua. We also evaluated how different varieties react to the same post-harvest procedures such as fermentation time, type of drying and roasting. The characterization of the metabolomic profile of seven different Arabica varieties (Bourbon-typica), allowed us also to assess the possible use of an NMR spectra of bean aqueous extracts to recognize the farm of origin, even considering different farms from the same geographical area (Nueva Segovia). Here, we also evaluated the effect of post-harvest procedures such as fermentation time and type of drying on green and roasted coffee, suggesting that post-harvest procedures can be responsible for different flavours. This study provides proof of concept for the ability of NMR to phenotype coffee, helping to authenticate and optimise the best way of processing coffee.
Keywords	metabolomics ; phenotyping ; nuclear magnetic resonance spectroscopy ; coffee beans ; coffee processing ; coffee varieties ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
Subject code	910
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: NMR-Based Metabolomics to Evaluate Individual Response to Treatments.

Vignoli, Alessia / Meoni, Gaia / Ghini, Veronica / Di Cesare, Francesca / Tenori, Leonardo / Luchinat, Claudio / Turano, Paola

Handbook of experimental pharmacology

2022 Volume 277, Page(s) 209–245

Abstract: The aim of this chapter is to highlight the various aspects of metabolomics in relation to health and diseases, starting from the definition of metabolic space and of how individuals tend to maintain their own position in this space. Physio-pathological ... ...

Abstract	The aim of this chapter is to highlight the various aspects of metabolomics in relation to health and diseases, starting from the definition of metabolic space and of how individuals tend to maintain their own position in this space. Physio-pathological stimuli may cause individuals to lose their position and then regain it, or move irreversibly to other positions. By way of examples, mostly selected from our own work using
MeSH term(s)	Humans ; Magnetic Resonance Spectroscopy ; Metabolomics ; Magnetic Resonance Imaging
Language	English
Publishing date	2022-11-01
Publishing country	Germany
Document type	Journal Article
ISSN	0171-2004
ISSN	0171-2004
DOI	10.1007/164_2022_618
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Article ; Online: Selenium Biofortification Impacts the Tomato Fruit Metabolome and Transcriptional Profile at Ripening.

Shiriaev, Anton / Brizzolara, Stefano / Sorce, Carlo / Meoni, Gaia / Vergata, Chiara / Martinelli, Federico / Maza, Elie / Djari, Anis / Pirrello, Julien / Pezzarossa, Beatrice / Malorgio, Fernando / Tonutti, Pietro

Journal of agricultural and food chemistry

2023 Volume 71, Issue 36, Page(s) 13554–13565

Abstract: In the present work, the effects of enriching tomatoes with selenium were studied in terms of physiological, metabolic, and molecular processes in the last stages of fruit development, particularly during ripening. A selenium concentration of 10 mg ... ...

Abstract	In the present work, the effects of enriching tomatoes with selenium were studied in terms of physiological, metabolic, and molecular processes in the last stages of fruit development, particularly during ripening. A selenium concentration of 10 mg L
MeSH term(s)	Selenium ; Solanum lycopersicum/genetics ; Biofortification ; Fruit/genetics ; Metabolome
Chemical Substances	Selenium (H6241UJ22B)
Language	English
Publishing date	2023-08-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	241619-0
ISSN	1520-5118 ; 0021-8561
ISSN (online)	1520-5118
ISSN	0021-8561
DOI	10.1021/acs.jafc.3c02031
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Article ; Online: From adenoma to CRC stages: the oral-gut microbiome axis as a source of potential microbial and metabolic biomarkers of malignancy.

Russo, Edda / Gloria, Leandro Di / Nannini, Giulia / Meoni, Gaia / Niccolai, Elena / Ringressi, Maria Novella / Baldi, Simone / Fani, Renato / Tenori, Leonardo / Taddei, Antonio / Ramazzotti, Matteo / Amedei, Amedeo

Neoplasia (New York, N.Y.)

2023 Volume 40, Page(s) 100901

Abstract: Background: Approximately 95% of Colorectal cancers (CRC) consist of adenocarcinomas originating from colonic Adenomatous polyps (AP). Increasing importance in CRC occurrence and progression has been attributed to the gut microbiota; however, a huge ... ...

Abstract	Background: Approximately 95% of Colorectal cancers (CRC) consist of adenocarcinomas originating from colonic Adenomatous polyps (AP). Increasing importance in CRC occurrence and progression has been attributed to the gut microbiota; however, a huge proportion of microorganisms inhabit the human digestive system. So, to comprehensively study the microbial spatial variations and their role in CRC progression, from AP to the different CRC phases, a holistic vision is imperative, including the simultaneous evaluation of multiple niches from the gastrointestinal system. Through an integrated approach, we identified potential microbial and metabolic biomarkers, able to discriminate human CRC from AP and/or also the different Tumor node metastasis (TNM) staging. In addition, as the microbiota contributes to the production of essential metabolic products detectable in fecal samples, we analysed and compared metabolites obtained from CRC and AP patients by using a Nuclear magnetic resonance (NMR) approach. Methods: In this observational study, saliva, tissue and stool samples from 61 patients, have been collected, including 46 CRC and 15 AP patients, age and sex-matched, undergoing surgery in 2018 at the Careggi University Hospital (Florence, Italy). First, the microbiota in the three-district between CRC and AP patients has been characterized, as well as in different CRC TNM stages. Subsequently, proton NMR spectroscopy has been used in combination with multivariate and univariate statistical approaches, to define the fecal metabolic profile of a restricted group of CRC and AP patients. Results: CRC patients display a different profile of tissue and fecal microbiota with respect to AP patients. Significant differences have been observed in CRC tissue microbial clades, with a rise of the Fusobacterium genus. In addition, significant taxa increase at the genus level has been observed in stool samples of CRC patients. Furthermore, Fusobacterium found in intestinal tissue has been positively correlated with fecal Parvimonas, for the first time. Moreover, as predicted by metagenomics pathway analysis, a significant increase of lactate (p=0.037) has been observed in the CRC fecal metabolic profiles, and positively correlated with Bifidobacterium (p=0.036). Finally, minor bacterial differences in CRC patients at stage T2 (TNM classification) have been detected, with a raise of the Spirochaetota phylum in CRC samples, with a slight increase of the Alphaproteobacteria class in fecal samples. Conclusion: Our results suggest the importance of microbiota communities and oncometabolites in CRC development. Further studies on CRC/AP management with a focus on CRC assessment are needed to investigate novel microbial-related diagnostic tools aimed to improve therapeutic interventions.
MeSH term(s)	Humans ; Gastrointestinal Microbiome ; Colorectal Neoplasms/pathology ; Adenoma/diagnosis ; Microbiota ; Bacteria ; Rectal Neoplasms ; Biomarkers
Chemical Substances	Biomarkers
Language	English
Publishing date	2023-04-12
Publishing country	United States
Document type	Observational Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1483840-0
ISSN	1476-5586 ; 1522-8002
ISSN (online)	1476-5586
ISSN	1522-8002
DOI	10.1016/j.neo.2023.100901
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Article ; Online: Metabolomics of gingival crevicular fluid to identify biomarkers for periodontitis: A systematic review with meta-analysis.

Baima, Giacomo / Corana, Matteo / Iaderosa, Giovanni / Romano, Federica / Citterio, Filippo / Meoni, Gaia / Tenori, Leonardo / Aimetti, Mario

Journal of periodontal research

2021 Volume 56, Issue 4, Page(s) 633–645

Abstract: The present systematic review aimed to examine periodontitis-specific biomarkers in the gingival crevicular fluid (GCF) that could have a diagnostic relevance, and to provide a qualitative assessment of the current literature. Metabolites are reliable ... ...

Abstract	The present systematic review aimed to examine periodontitis-specific biomarkers in the gingival crevicular fluid (GCF) that could have a diagnostic relevance, and to provide a qualitative assessment of the current literature. Metabolites are reliable indicators of pathophysiological statuses, and their quantification in the GCF can provide an outlook of the changes associated with periodontitis and have diagnostic value. Relevant studies identified from PubMed, Embase, Cochrane Library, and Scopus databases were examined to answer the following PECO question: "In systemically healthy individuals, can concentration of specific metabolites in the GCF be used to discriminate subjects with healthy periodontium (H) or gingivitis from patients with periodontitis (P) and which is the diagnostic accuracy?" Quality of included studies was rated using a modified version of the QUADOMICS tool. Meta-analysis was conducted whenever possible. After the screening of 1,554 titles, 15 studies were selected, with sample size ranging from 30 to 93 subjects. Eleven studies performed targeted metabolomics analysis and provided data for 10 metabolites. Among the most consistent markers, malondialdehyde levels were found higher in the P group compared with H group (SMD = 2.86; 95% CI: 1.64, 4.08). Also, a significant increase of 8-hydroxy-deoxyguanosine, 4-hydroxynonenal, and neopterin was detected in periodontally diseased sites, while glutathione showed an inverse trend. When considering data from untargeted metabolomic analysis in four studies, more than 40 metabolites were found significantly discriminant, mainly related to amino acids and lipids degradation pathways. Notably, only one study reported measures of diagnostic accuracy. Several metabolites were differentially expressed in GCF of subjects across different periodontal conditions, having a major potential for investigating periodontal pathophysiology and for site-specific diagnosis. Oxidative stress-related molecules, such as malondialdehyde and 8-hydroxy-deoxyguanosine, were the most consistently associated to periodontitis (PROSPERO CRD42020188482).
Language	English
Publishing date	2021-03-12
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	390953-0
ISSN	1600-0765 ; 0022-3484
ISSN (online)	1600-0765
ISSN	0022-3484
DOI	10.1111/jre.12872
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