NMR-based metabolomics and fluxomics: developments and future prospects

Giraudeau, Patrick

doi:10.1039/d0an00142b

Cited by 63 publications

(77 citation statements)

References 131 publications

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“…In contrast, NMR can provide a simpler, more reproducible method for quantitative molecule detection, albeit with considerably lower sensitivity. NMR does not require the same laborious sample preparation that MS does, and the sample can remain intact throughout the analysis, thus making it a better quantitative tool [ 19 , 20 , 21 , 22 , 23 , 24 ]. However, for reasons of practicality and health and safety, NMR methods still require the extraction of metabolites from semi-solid samples such as cell cultures, as high resolution 1 H NMR is a solution state method.…”

Section: Introductionmentioning

confidence: 99%

Establishing a Metabolite Extraction Method to Study the Metabolome of Blastocystis Using NMR

et al. 2021

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Blastocystis is an opportunistic parasite commonly found in the intestines of humans and other animals. Despite its high prevalence, knowledge regarding Blastocystis biology within and outside the host is limited. Analysis of the metabolites produced by this anaerobe could provide insights that can help map its metabolism and determine its role in both health and disease. Due to its controversial pathogenicity, these metabolites could define its deterministic role in microbiome’s “health” and/or subsequently resolve Blastocystis’ potential impact in gastrointestinal health. A common method for elucidating the presence of these metabolites is through 1H nuclear magnetic resonance (NMR). However, there are currently no described benchmarked methods available to extract metabolites from Blastocystis for 1H NMR analysis. Herein, several extraction solvents, lysis methods and incubation temperatures were compared for their usefulness as an extraction protocol for this protozoan. Following extraction, the samples were freeze-dried, re-solubilized and analysed with 1H NMR. The results demonstrate that carrying out the procedure at room temperature using methanol as an extraction solvent and bead bashing as a lysis technique provides a consistent, reproducible and efficient method to extract metabolites from Blastocystis for NMR.

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Section: Introductionmentioning

confidence: 99%

Establishing a Metabolite Extraction Method to Study the Metabolome of Blastocystis Using NMR

et al. 2021

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“…Nuclear magnetic resonance (NMR) spectroscopy is a powerful analytical technique for high-throughput metabolic fingerprinting and provides more reliable metabolite structure (e.g., via 2D NMR) identification than MS (Giraudeau, 2020). However, although NMR offers unambiguous structure determination of unknown metabolites via 1 H-and 13 C-NMR, MS-based methods comprise widely accessed metabolomics techniques due to higher sensitivity and lower instrumentation cost (Chatham and Blackband, 2001).…”

Section: Metabolomicsmentioning

confidence: 99%

Omics-Driven Biotechnology for Industrial Applications

Amer

Baidoo

2021

Front. Bioeng. Biotechnol.

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Biomanufacturing is a key component of biotechnology that uses biological systems to produce bioproducts of commercial relevance, which are of great interest to the energy, material, pharmaceutical, food, and agriculture industries. Biotechnology-based approaches, such as synthetic biology and metabolic engineering are heavily reliant on “omics” driven systems biology to characterize and understand metabolic networks. Knowledge gained from systems biology experiments aid the development of synthetic biology tools and the advancement of metabolic engineering studies toward establishing robust industrial biomanufacturing platforms. In this review, we discuss recent advances in “omics” technologies, compare the pros and cons of the different “omics” technologies, and discuss the necessary requirements for carrying out multi-omics experiments. We highlight the influence of “omics” technologies on the production of biofuels and bioproducts by metabolic engineering. Finally, we discuss the application of “omics” technologies to agricultural and food biotechnology, and review the impact of “omics” on current COVID-19 research.

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“…Since spectra are highly crowded, the potential of these methods could be significantly boosted by relying on acquisition strategies that better separate peaks at the acquisition stage of the analytical workflow. At high field, the potential of UF 2D and pure-shift NMR approaches in ''omics" workflows has been demonstrated in a number of cases [71]. At medium field, this potential is even higher since peak overlap is even more critical.…”

Section: Application To Authenticationmentioning

confidence: 99%

Gradient-based pulse sequences for benchtop NMR spectroscopy

Gouilleux

Farjon

Giraudeau

2020

Journal of Magnetic Resonance

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Benchtop NMR spectroscopy has been on the rise for the last decade, by bringing high-resolution NMR in 30 environments that are not easily compatible with high-field NMR. Benchtop spectrometers are accessible, 31 low cost and show an impressive performance in terms of sensitivity with respect to the relatively low 32 associated magnetic field (40-100 MHz). However, their application is limited by the strong and ubiqui-33 tous peak overlaps arising from the complex mixtures which are often targeted, often characterized by a 34 great diversity of concentrations and by strong signals from non-deuterated solvents. Such limitations 35 can be addressed by pulse sequences making clever use of magnetic field gradient pulses, capable of per-36 forming efficient coherence selection or encoding chemical shift or diffusion information. Gradients 37 pulses are well-known ingredients of high-field pulse sequence recipes, but were only recently made 38 available on benchtop spectrometers, thanks to the introduction of gradient coils in 2015. This article 39 reviews the recent methodological advances making use of gradient pulses on benchtop spectrometers 40 and the applications stemming from these developments. Particular focus is made on solvent suppression 41 schemes, diffusion-encoded, and spatially-encoded experiments, while discussing both methodological 42 advances and subsequent applications. We eventually discuss the exciting development and application 43 perspectives that result from such advances.

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NMR-based metabolomics and fluxomics: developments and future prospects

Abstract: Recent NMR developments are acting as game changers for metabolomics and fluxomics – a critical and perspective review.

Cited by 63 publications

References 131 publications

Establishing a Metabolite Extraction Method to Study the Metabolome of Blastocystis Using NMR

Establishing a Metabolite Extraction Method to Study the Metabolome of Blastocystis Using NMR

Omics-Driven Biotechnology for Industrial Applications

Gradient-based pulse sequences for benchtop NMR spectroscopy

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